ADL: viewing results

classic Classic list List threaded Threaded
28 messages Options
12
Reply | Threaded
Open this post in threaded view
|

ADL: viewing results

Dvořáková Marcela UEB
Hi,


may anyone advise me on how to view te vina results in Ligandscout? I got through the pdf tutorial but I did not get it. I am using just the free 30-days trial version of Ligandscout.


Or may anyone suggest another program (for windows) which would nicely display the interactions of ligand with protein (polar as well as hydrophobic)?


Thanks, Marcela

Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného návrhu na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu experimentální botaniky AV ČR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message cannot be considered as a proposal to conclude a contract, neither the acceptance of a proposal to conclude a contract, nor does it create any pre-contractual liability on the part of the Institute of experimental botany of the CAS, v. v. i.
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Hello
I will suggest you to use Chimera it is free available for windows and
unlimited without any trial period. I am using it myslef.

On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <[hidden email]
> wrote:

> Hi,
>
>
> may anyone advise me on how to view te vina results in Ligandscout? I got
> through the pdf tutorial but I did not get it. I am using just the free
> 30-days trial version of Ligandscout.
>
>
> Or may anyone suggest another program (for windows) which would nicely
> display the interactions of ligand with protein (polar as well as
> hydrophobic)?
>
>
> Thanks, Marcela
>
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného návrhu
> na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> experimentální botaniky AV ČR, v. v. i.
>
> Disclaimer: If not expressly stated otherwise, this e-mail message cannot
> be considered as a proposal to conclude a contract, neither the acceptance
> of a proposal to conclude a contract, nor does it create any
> pre-contractual liability on the part of the Institute of experimental
> botany of the CAS, v. v. i.
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Diogo Martins
I suggest these two:

pymol: https://sourceforge.net/projects/pymol/
pmv (part of MGLTools): http://mgltools.scripps.edu/downloads

On 13 November 2017 at 03:52, bushra TAJ <[hidden email]> wrote:

> Hello
> I will suggest you to use Chimera it is free available for windows and
> unlimited without any trial period. I am using it myslef.
>
> On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <
> [hidden email]
> > wrote:
>
> > Hi,
> >
> >
> > may anyone advise me on how to view te vina results in Ligandscout? I got
> > through the pdf tutorial but I did not get it. I am using just the free
> > 30-days trial version of Ligandscout.
> >
> >
> > Or may anyone suggest another program (for windows) which would nicely
> > display the interactions of ligand with protein (polar as well as
> > hydrophobic)?
> >
> >
> > Thanks, Marcela
> >
> > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
> návrhu
> > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> > experimentální botaniky AV ČR, v. v. i.
> >
> > Disclaimer: If not expressly stated otherwise, this e-mail message cannot
> > be considered as a proposal to conclude a contract, neither the
> acceptance
> > of a proposal to conclude a contract, nor does it create any
> > pre-contractual liability on the part of the Institute of experimental
> > botany of the CAS, v. v. i.
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Dvořáková Marcela UEB
Hi, thanks for the suggestions...

I use pymol, but it shows only polar contacts...I would like to see also the hydrophobic contacts...

I downloaded chimera, but I do not know how to display the vina results there showing the contacts.


________________________________
Od: [hidden email] <[hidden email]> za uživatele Diogo Martins <[hidden email]>
Odesláno: pondělí 13. listopadu 2017 20:47
Komu: [hidden email]
Předmět: Re: ADL: viewing results

I suggest these two:

pymol: https://sourceforge.net/projects/pymol/
[https://a.fsdn.com/allura/p/pymol/icon?1491835960]<https://sourceforge.net/projects/pymol/>

PyMOL Molecular Graphics System download | SourceForge.net<https://sourceforge.net/projects/pymol/>
sourceforge.net
Download PyMOL Molecular Graphics System for free. PyMOL is an OpenGL based molecular visualization system. PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories.


pmv (part of MGLTools): http://mgltools.scripps.edu/downloads

On 13 November 2017 at 03:52, bushra TAJ <[hidden email]> wrote:

> Hello
> I will suggest you to use Chimera it is free available for windows and
> unlimited without any trial period. I am using it myslef.
>
> On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <
> [hidden email]
> > wrote:
>
> > Hi,
> >
> >
> > may anyone advise me on how to view te vina results in Ligandscout? I got
> > through the pdf tutorial but I did not get it. I am using just the free
> > 30-days trial version of Ligandscout.
> >
> >
> > Or may anyone suggest another program (for windows) which would nicely
> > display the interactions of ligand with protein (polar as well as
> > hydrophobic)?
> >
> >
> > Thanks, Marcela
> >
> > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
> návrhu
> > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> > experimentální botaniky AV ČR, v. v. i.
> >
> > Disclaimer: If not expressly stated otherwise, this e-mail message cannot
> > be considered as a proposal to conclude a contract, neither the
> acceptance
> > of a proposal to conclude a contract, nor does it create any
> > pre-contractual liability on the part of the Institute of experimental
> > botany of the CAS, v. v. i.
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
AutoDock Mailing List — AutoDock<http://autodock.scripps.edu/mailing_list>
autodock.scripps.edu
AutoDock web site


> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
AutoDock Mailing List — AutoDock<http://autodock.scripps.edu/mailing_list>
autodock.scripps.edu
AutoDock web site


>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
AutoDock Mailing List — AutoDock<http://autodock.scripps.edu/mailing_list>
autodock.scripps.edu
AutoDock web site


Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného návrhu na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu experimentální botaniky AV ČR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message cannot be considered as a proposal to conclude a contract, neither the acceptance of a proposal to conclude a contract, nor does it create any pre-contractual liability on the part of the Institute of experimental botany of the CAS, v. v. i.
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Hello You must have exported your vina docked conformation (the best one)
in pdb format just load that pdb file in chimera
Hope it will help
Rregards


On Tue, Nov 14, 2017 at 1:14 PM, Dvořáková Marcela UEB <[hidden email]
> wrote:

> Hi, thanks for the suggestions...
>
> I use pymol, but it shows only polar contacts...I would like to see also
> the hydrophobic contacts...
>
> I downloaded chimera, but I do not know how to display the vina results
> there showing the contacts.
>
>
> ________________________________
> Od: [hidden email] <[hidden email]> za
> uživatele Diogo Martins <[hidden email]>
> Odesláno: pondělí 13. listopadu 2017 20:47
> Komu: [hidden email]
> Předmět: Re: ADL: viewing results
>
> I suggest these two:
>
> pymol: https://sourceforge.net/projects/pymol/
> [https://a.fsdn.com/allura/p/pymol/icon?1491835960]<https:/
> /sourceforge.net/projects/pymol/>
>
> PyMOL Molecular Graphics System download | SourceForge.net<https://
> sourceforge.net/projects/pymol/>
> sourceforge.net
> Download PyMOL Molecular Graphics System for free. PyMOL is an OpenGL
> based molecular visualization system. PyMOL is a Python-enhanced molecular
> graphics tool. It excels at 3D visualization of proteins, small molecules,
> density, surfaces, and trajectories.
>
>
> pmv (part of MGLTools): http://mgltools.scripps.edu/downloads
>
> On 13 November 2017 at 03:52, bushra TAJ <[hidden email]> wrote:
>
> > Hello
> > I will suggest you to use Chimera it is free available for windows and
> > unlimited without any trial period. I am using it myslef.
> >
> > On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <
> > [hidden email]
> > > wrote:
> >
> > > Hi,
> > >
> > >
> > > may anyone advise me on how to view te vina results in Ligandscout? I
> got
> > > through the pdf tutorial but I did not get it. I am using just the free
> > > 30-days trial version of Ligandscout.
> > >
> > >
> > > Or may anyone suggest another program (for windows) which would nicely
> > > display the interactions of ligand with protein (polar as well as
> > > hydrophobic)?
> > >
> > >
> > > Thanks, Marcela
> > >
> > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> > > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
> > návrhu
> > > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> > > experimentální botaniky AV ČR, v. v. i.
> > >
> > > Disclaimer: If not expressly stated otherwise, this e-mail message
> cannot
> > > be considered as a proposal to conclude a contract, neither the
> > acceptance
> > > of a proposal to conclude a contract, nor does it create any
> > > pre-contractual liability on the part of the Institute of experimental
> > > botany of the CAS, v. v. i.
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> AutoDock Mailing List — AutoDock<http://autodock.scripps.edu/mailing_list>
> autodock.scripps.edu
> AutoDock web site
>
>
> > >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> AutoDock Mailing List — AutoDock<http://autodock.scripps.edu/mailing_list>
> autodock.scripps.edu
> AutoDock web site
>
>
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> AutoDock Mailing List — AutoDock<http://autodock.scripps.edu/mailing_list>
> autodock.scripps.edu
> AutoDock web site
>
>
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného návrhu
> na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> experimentální botaniky AV ČR, v. v. i.
>
> Disclaimer: If not expressly stated otherwise, this e-mail message cannot
> be considered as a proposal to conclude a contract, neither the acceptance
> of a proposal to conclude a contract, nor does it create any
> pre-contractual liability on the part of the Institute of experimental
> botany of the CAS, v. v. i.
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Jakubowski, Henry
In reply to this post by Dvořáková Marcela UEB
Hello,



I think what she means is how to analyze a pdb file generated by Autodock vina for intermolecular forces involved in ligand/protein interactions.



Chimera is great for display but I don't think it works very well for the visual analysis of IMFs.  You can choose Tools, Surface Binding Analyses, Find H bonds, for example, but the output is not robust as when you used the PDBs ligand explorer for analyzing PDB files downloaded directly from the PDB.



Ligand Explorer doesn't work (for me anyway) with PDB files derived from Autodock Vina or from those files uploaded first into Chimera, saved and then analyzed by Ligand Explorer.



I have my students use VMD<http://www.ks.uiuc.edu/Research/vmd/> for the analyses of IMFs.  I've pasted the instructions below.  They are a bit convoluted.



  1.  Load your docked ligand/protein complex into VMD (File, New Molecule, Browse ..).
  2.  In the VMD Main window select Extensions, TK console.
  3.  To find out what directory you are in, type     ls        (for list)
  4.  Next type    cd ..   (that is cd space dot dot) to change directories (cd) to the directory above the one you are in at present.  Type   ls   again.
  5.  Repeat cd and ls until when you type  ls you find the folder Users/
  6.  Type in cd Users to see the individual user folder (it's case sensitive)
  7.  Type   ls to see the folders
  8.  Type cd yourusername to move to your folder, and  then ls  is see what's in your folder..
  9.  [if you are using your own PC, type cd Documents to get to your document folder or if you can't find that cd Desktop.)  If you are using a networked PC, just stay in your username folder.
  10. Now create a variable (csn) that will store the protein:ligand structure coordinates by typing the follow:  set csn [atomselect top all]      (this will save protein and ligand coordinates)
  11. Finally type   $csn writepdb csnall.pdb
You should be able to find it in the following folder:  M:\CitrixProfile\UPM_Profile\Downloads.  It might take a few minutes for it to appear however.  It might appear in the Citrix/Pending folder.

Save the file in one of your regular folders.  Go to Protein Ligand Interaction Profiler<https://projects.biotec.tu-dresden.de/plip-web/plip/index>.  Upload your file by browsing to your file.  Submit the file and visualize the results when finished (as illustrated below)
[cid:image003.jpg@01D35D0D.683C32D0]









You will see a table detailing the ligand:protein interactions.



Does anyone have a better way to visually analyze the docked ligand:protein IMFs?  (i.e is there an external program designed specifically to analyze the IMFs that works on pdb files saved by autodock vina?



Thanks

Henry Jakubowski


.
Chemistry Department
College of St. Benedict/St. John's University
37 S. College Ave.
St. Joseph, MN 56374

e:  [hidden email]<mailto:[hidden email]>
w:  http://employees.csbsju.edu/hjakubowski
Biochemistry Online:  An Approach Based on Chemical Logic<http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html>






-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Dvoráková Marcela UEB
Sent: Tuesday, November 14, 2017 2:15 AM
To: [hidden email]
Subject: Re: ADL: viewing results



Hi, thanks for the suggestions...



I use pymol, but it shows only polar contacts...I would like to see also the hydrophobic contacts...



I downloaded chimera, but I do not know how to display the vina results there showing the contacts.





________________________________

Od: [hidden email]<mailto:[hidden email]> <[hidden email]<mailto:[hidden email]>> za uživatele Diogo Martins <[hidden email]<mailto:[hidden email]>>

Odesláno: pondělí 13. listopadu 2017 20:47

Komu: [hidden email]<mailto:[hidden email]>

Předmět: Re: ADL: viewing results



I suggest these two:



pymol: https://sourceforge.net/projects/pymol/

[https://a.fsdn.com/allura/p/pymol/icon?1491835960]<https://sourceforge.net/projects/pymol/>



PyMOL Molecular Graphics System download | SourceForge.net<https://sourceforge.net/projects/pymol/>

sourceforge.net

Download PyMOL Molecular Graphics System for free. PyMOL is an OpenGL based molecular visualization system. PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories.





pmv (part of MGLTools): http://mgltools.scripps.edu/downloads



On 13 November 2017 at 03:52, bushra TAJ <[hidden email]<mailto:[hidden email]>> wrote:



> Hello

> I will suggest you to use Chimera it is free available for windows and

> unlimited without any trial period. I am using it myslef.

>

> On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <

> [hidden email]<mailto:[hidden email]>

> > wrote:

>

> > Hi,

> >

> >

> > may anyone advise me on how to view te vina results in Ligandscout?

> > I got through the pdf tutorial but I did not get it. I am using just

> > the free 30-days trial version of Ligandscout.

> >

> >

> > Or may anyone suggest another program (for windows) which would

> > nicely display the interactions of ligand with protein (polar as

> > well as hydrophobic)?

> >

> >

> > Thanks, Marcela

> >

> > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato

> > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného

> návrhu

> > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu

> > experimentální botaniky AV ČR, v. v. i.

> >

> > Disclaimer: If not expressly stated otherwise, this e-mail message

> > cannot be considered as a proposal to conclude a contract, neither

> > the

> acceptance

> > of a proposal to conclude a contract, nor does it create any

> > pre-contractual liability on the part of the Institute of

> > experimental botany of the CAS, v. v. i.

> > ________________________________________________

> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list

> > ---

AutoDock Mailing List - AutoDock<http://autodock.scripps.edu/mailing_list>

autodock.scripps.edu

AutoDock web site





> >

> ________________________________________________

> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list

> ---

AutoDock Mailing List - AutoDock<http://autodock.scripps.edu/mailing_list>

autodock.scripps.edu

AutoDock web site





>

________________________________________________

--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list --- AutoDock Mailing List - AutoDock<http://autodock.scripps.edu/mailing_list>

autodock.scripps.edu

AutoDock web site





Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného návrhu na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu experimentální botaniky AV ČR, v. v. i.



Disclaimer: If not expressly stated otherwise, this e-mail message cannot be considered as a proposal to conclude a contract, neither the acceptance of a proposal to conclude a contract, nor does it create any pre-contractual liability on the part of the Institute of experimental botany of the CAS, v. v. i.

________________________________________________

--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---

________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Hello
Is that OK to analyse binding modes and distances using Chimera?? cant we
report it as authentic??
Is VMD the only options for windows OS??
Regards

On Tue, Nov 14, 2017 at 3:57 AM, Jakubowski, Henry <[hidden email]>
wrote:

> Hello,
>
>
>
> I think what she means is how to analyze a pdb file generated by Autodock
> vina for intermolecular forces involved in ligand/protein interactions.
>
>
>
> Chimera is great for display but I don't think it works very well for the
> visual analysis of IMFs.  You can choose Tools, Surface Binding Analyses,
> Find H bonds, for example, but the output is not robust as when you used
> the PDBs ligand explorer for analyzing PDB files downloaded directly from
> the PDB.
>
>
>
> Ligand Explorer doesn't work (for me anyway) with PDB files derived from
> Autodock Vina or from those files uploaded first into Chimera, saved and
> then analyzed by Ligand Explorer.
>
>
>
> I have my students use VMD<http://www.ks.uiuc.edu/Research/vmd/> for the
> analyses of IMFs.  I've pasted the instructions below.  They are a bit
> convoluted.
>
>
>
>   1.  Load your docked ligand/protein complex into VMD (File, New
> Molecule, Browse ..).
>   2.  In the VMD Main window select Extensions, TK console.
>   3.  To find out what directory you are in, type     ls        (for list)
>   4.  Next type    cd ..   (that is cd space dot dot) to change
> directories (cd) to the directory above the one you are in at present.
> Type   ls   again.
>   5.  Repeat cd and ls until when you type  ls you find the folder Users/
>   6.  Type in cd Users to see the individual user folder (it's case
> sensitive)
>   7.  Type   ls to see the folders
>   8.  Type cd yourusername to move to your folder, and  then ls  is see
> what's in your folder..
>   9.  [if you are using your own PC, type cd Documents to get to your
> document folder or if you can't find that cd Desktop.)  If you are using a
> networked PC, just stay in your username folder.
>   10. Now create a variable (csn) that will store the protein:ligand
> structure coordinates by typing the follow:  set csn [atomselect top all]
>     (this will save protein and ligand coordinates)
>   11. Finally type   $csn writepdb csnall.pdb
> You should be able to find it in the following folder:
> M:\CitrixProfile\UPM_Profile\Downloads.  It might take a few minutes for
> it to appear however.  It might appear in the Citrix/Pending folder.
>
> Save the file in one of your regular folders.  Go to Protein Ligand
> Interaction Profiler<https://projects.biotec.tu-dresden.de/plip-web/
> plip/index>.  Upload your file by browsing to your file.  Submit the file
> and visualize the results when finished (as illustrated below)
> [cid:image003.jpg@01D35D0D.683C32D0]
>
>
>
>
>
>
>
>
>
> You will see a table detailing the ligand:protein interactions.
>
>
>
> Does anyone have a better way to visually analyze the docked
> ligand:protein IMFs?  (i.e is there an external program designed
> specifically to analyze the IMFs that works on pdb files saved by autodock
> vina?
>
>
>
> Thanks
>
> Henry Jakubowski
>
>
> .
> Chemistry Department
> College of St. Benedict/St. John's University
> 37 S. College Ave.
> St. Joseph, MN 56374
>
> e:  [hidden email]<mailto:[hidden email]>
> w:  http://employees.csbsju.edu/hjakubowski
> Biochemistry Online:  An Approach Based on Chemical Logic<
> http://employees.csbsju.edu/hjakubowski/classes/ch331/bcintro/default.html
> >
>
>
>
>
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]]
> On Behalf Of Dvoráková Marcela UEB
> Sent: Tuesday, November 14, 2017 2:15 AM
> To: [hidden email]
> Subject: Re: ADL: viewing results
>
>
>
> Hi, thanks for the suggestions...
>
>
>
> I use pymol, but it shows only polar contacts...I would like to see also
> the hydrophobic contacts...
>
>
>
> I downloaded chimera, but I do not know how to display the vina results
> there showing the contacts.
>
>
>
>
>
> ________________________________
>
> Od: [hidden email]<mailto:[hidden email]> <
> [hidden email]<mailto:[hidden email]>> za
> uživatele Diogo Martins <[hidden email]<mailto:
> [hidden email]>>
>
> Odesláno: pondělí 13. listopadu 2017 20:47
>
> Komu: [hidden email]<mailto:[hidden email]>
>
> Předmět: Re: ADL: viewing results
>
>
>
> I suggest these two:
>
>
>
> pymol: https://sourceforge.net/projects/pymol/
>
> [https://a.fsdn.com/allura/p/pymol/icon?1491835960]<https:/
> /sourceforge.net/projects/pymol/>
>
>
>
> PyMOL Molecular Graphics System download | SourceForge.net<https://
> sourceforge.net/projects/pymol/>
>
> sourceforge.net
>
> Download PyMOL Molecular Graphics System for free. PyMOL is an OpenGL
> based molecular visualization system. PyMOL is a Python-enhanced molecular
> graphics tool. It excels at 3D visualization of proteins, small molecules,
> density, surfaces, and trajectories.
>
>
>
>
>
> pmv (part of MGLTools): http://mgltools.scripps.edu/downloads
>
>
>
> On 13 November 2017 at 03:52, bushra TAJ <[hidden email]<mailto:
> [hidden email]>> wrote:
>
>
>
> > Hello
>
> > I will suggest you to use Chimera it is free available for windows and
>
> > unlimited without any trial period. I am using it myslef.
>
> >
>
> > On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <
>
> > [hidden email]<mailto:[hidden email]>
>
> > > wrote:
>
> >
>
> > > Hi,
>
> > >
>
> > >
>
> > > may anyone advise me on how to view te vina results in Ligandscout?
>
> > > I got through the pdf tutorial but I did not get it. I am using just
>
> > > the free 30-days trial version of Ligandscout.
>
> > >
>
> > >
>
> > > Or may anyone suggest another program (for windows) which would
>
> > > nicely display the interactions of ligand with protein (polar as
>
> > > well as hydrophobic)?
>
> > >
>
> > >
>
> > > Thanks, Marcela
>
> > >
>
> > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
>
> > > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
>
> > návrhu
>
> > > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
>
> > > experimentální botaniky AV ČR, v. v. i.
>
> > >
>
> > > Disclaimer: If not expressly stated otherwise, this e-mail message
>
> > > cannot be considered as a proposal to conclude a contract, neither
>
> > > the
>
> > acceptance
>
> > > of a proposal to conclude a contract, nor does it create any
>
> > > pre-contractual liability on the part of the Institute of
>
> > > experimental botany of the CAS, v. v. i.
>
> > > ________________________________________________
>
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>
> > > ---
>
> AutoDock Mailing List - AutoDock<http://autodock.scripps.edu/mailing_list>
>
> autodock.scripps.edu
>
> AutoDock web site
>
>
>
>
>
> > >
>
> > ________________________________________________
>
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>
> > ---
>
> AutoDock Mailing List - AutoDock<http://autodock.scripps.edu/mailing_list>
>
> autodock.scripps.edu
>
> AutoDock web site
>
>
>
>
>
> >
>
> ________________________________________________
>
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> AutoDock Mailing List - AutoDock<http://autodock.scripps.edu/mailing_list>
>
> autodock.scripps.edu
>
> AutoDock web site
>
>
>
>
>
> Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného návrhu
> na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> experimentální botaniky AV ČR, v. v. i.
>
>
>
> Disclaimer: If not expressly stated otherwise, this e-mail message cannot
> be considered as a proposal to conclude a contract, neither the acceptance
> of a proposal to conclude a contract, nor does it create any
> pre-contractual liability on the part of the Institute of experimental
> botany of the CAS, v. v. i.
>
> ________________________________________________
>
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Diogo Martins
Hello,

Any viewer is OK.

Cheers

On Nov 14, 2017 9:15 PM, "bushra TAJ" <[hidden email]> wrote:

> Hello
> Is that OK to analyse binding modes and distances using Chimera?? cant we
> report it as authentic??
> Is VMD the only options for windows OS??
> Regards
>
> On Tue, Nov 14, 2017 at 3:57 AM, Jakubowski, Henry <[hidden email]
> >
> wrote:
>
> > Hello,
> >
> >
> >
> > I think what she means is how to analyze a pdb file generated by Autodock
> > vina for intermolecular forces involved in ligand/protein interactions.
> >
> >
> >
> > Chimera is great for display but I don't think it works very well for the
> > visual analysis of IMFs.  You can choose Tools, Surface Binding Analyses,
> > Find H bonds, for example, but the output is not robust as when you used
> > the PDBs ligand explorer for analyzing PDB files downloaded directly from
> > the PDB.
> >
> >
> >
> > Ligand Explorer doesn't work (for me anyway) with PDB files derived from
> > Autodock Vina or from those files uploaded first into Chimera, saved and
> > then analyzed by Ligand Explorer.
> >
> >
> >
> > I have my students use VMD<http://www.ks.uiuc.edu/Research/vmd/> for the
> > analyses of IMFs.  I've pasted the instructions below.  They are a bit
> > convoluted.
> >
> >
> >
> >   1.  Load your docked ligand/protein complex into VMD (File, New
> > Molecule, Browse ..).
> >   2.  In the VMD Main window select Extensions, TK console.
> >   3.  To find out what directory you are in, type     ls        (for
> list)
> >   4.  Next type    cd ..   (that is cd space dot dot) to change
> > directories (cd) to the directory above the one you are in at present.
> > Type   ls   again.
> >   5.  Repeat cd and ls until when you type  ls you find the folder Users/
> >   6.  Type in cd Users to see the individual user folder (it's case
> > sensitive)
> >   7.  Type   ls to see the folders
> >   8.  Type cd yourusername to move to your folder, and  then ls  is see
> > what's in your folder..
> >   9.  [if you are using your own PC, type cd Documents to get to your
> > document folder or if you can't find that cd Desktop.)  If you are using
> a
> > networked PC, just stay in your username folder.
> >   10. Now create a variable (csn) that will store the protein:ligand
> > structure coordinates by typing the follow:  set csn [atomselect top all]
> >     (this will save protein and ligand coordinates)
> >   11. Finally type   $csn writepdb csnall.pdb
> > You should be able to find it in the following folder:
> > M:\CitrixProfile\UPM_Profile\Downloads.  It might take a few minutes for
> > it to appear however.  It might appear in the Citrix/Pending folder.
> >
> > Save the file in one of your regular folders.  Go to Protein Ligand
> > Interaction Profiler<https://projects.biotec.tu-dresden.de/plip-web/
> > plip/index>.  Upload your file by browsing to your file.  Submit the file
> > and visualize the results when finished (as illustrated below)
> > [cid:image003.jpg@01D35D0D.683C32D0]
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > You will see a table detailing the ligand:protein interactions.
> >
> >
> >
> > Does anyone have a better way to visually analyze the docked
> > ligand:protein IMFs?  (i.e is there an external program designed
> > specifically to analyze the IMFs that works on pdb files saved by
> autodock
> > vina?
> >
> >
> >
> > Thanks
> >
> > Henry Jakubowski
> >
> >
> > .
> > Chemistry Department
> > College of St. Benedict/St. John's University
> > 37 S. College Ave.
> > St. Joseph, MN 56374
> >
> > e:  [hidden email]<mailto:[hidden email]>
> > w:  http://employees.csbsju.edu/hjakubowski
> > Biochemistry Online:  An Approach Based on Chemical Logic<
> > http://employees.csbsju.edu/hjakubowski/classes/ch331/
> bcintro/default.html
> > >
> >
> >
> >
> >
> >
> >
> > -----Original Message-----
> > From: [hidden email] [mailto:[hidden email]]
> > On Behalf Of Dvoráková Marcela UEB
> > Sent: Tuesday, November 14, 2017 2:15 AM
> > To: [hidden email]
> > Subject: Re: ADL: viewing results
> >
> >
> >
> > Hi, thanks for the suggestions...
> >
> >
> >
> > I use pymol, but it shows only polar contacts...I would like to see also
> > the hydrophobic contacts...
> >
> >
> >
> > I downloaded chimera, but I do not know how to display the vina results
> > there showing the contacts.
> >
> >
> >
> >
> >
> > ________________________________
> >
> > Od: [hidden email]<mailto:[hidden email]> <
> > [hidden email]<mailto:[hidden email]>> za
> > uživatele Diogo Martins <[hidden email]<mailto:
> > [hidden email]>>
> >
> > Odesláno: pondělí 13. listopadu 2017 20:47
> >
> > Komu: [hidden email]<mailto:[hidden email]>
> >
> > Předmět: Re: ADL: viewing results
> >
> >
> >
> > I suggest these two:
> >
> >
> >
> > pymol: https://sourceforge.net/projects/pymol/
> >
> > [https://a.fsdn.com/allura/p/pymol/icon?1491835960]<https:/
> > /sourceforge.net/projects/pymol/>
> >
> >
> >
> > PyMOL Molecular Graphics System download | SourceForge.net<https://
> > sourceforge.net/projects/pymol/>
> >
> > sourceforge.net
> >
> > Download PyMOL Molecular Graphics System for free. PyMOL is an OpenGL
> > based molecular visualization system. PyMOL is a Python-enhanced
> molecular
> > graphics tool. It excels at 3D visualization of proteins, small
> molecules,
> > density, surfaces, and trajectories.
> >
> >
> >
> >
> >
> > pmv (part of MGLTools): http://mgltools.scripps.edu/downloads
> >
> >
> >
> > On 13 November 2017 at 03:52, bushra TAJ <[hidden email]<mailto:
> > [hidden email]>> wrote:
> >
> >
> >
> > > Hello
> >
> > > I will suggest you to use Chimera it is free available for windows and
> >
> > > unlimited without any trial period. I am using it myslef.
> >
> > >
> >
> > > On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <
> >
> > > [hidden email]<mailto:[hidden email]>
> >
> > > > wrote:
> >
> > >
> >
> > > > Hi,
> >
> > > >
> >
> > > >
> >
> > > > may anyone advise me on how to view te vina results in Ligandscout?
> >
> > > > I got through the pdf tutorial but I did not get it. I am using just
> >
> > > > the free 30-days trial version of Ligandscout.
> >
> > > >
> >
> > > >
> >
> > > > Or may anyone suggest another program (for windows) which would
> >
> > > > nicely display the interactions of ligand with protein (polar as
> >
> > > > well as hydrophobic)?
> >
> > > >
> >
> > > >
> >
> > > > Thanks, Marcela
> >
> > > >
> >
> > > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> >
> > > > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
> >
> > > návrhu
> >
> > > > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> >
> > > > experimentální botaniky AV ČR, v. v. i.
> >
> > > >
> >
> > > > Disclaimer: If not expressly stated otherwise, this e-mail message
> >
> > > > cannot be considered as a proposal to conclude a contract, neither
> >
> > > > the
> >
> > > acceptance
> >
> > > > of a proposal to conclude a contract, nor does it create any
> >
> > > > pre-contractual liability on the part of the Institute of
> >
> > > > experimental botany of the CAS, v. v. i.
> >
> > > > ________________________________________________
> >
> > > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> >
> > > > ---
> >
> > AutoDock Mailing List - AutoDock<http://autodock.
> scripps.edu/mailing_list>
> >
> > autodock.scripps.edu
> >
> > AutoDock web site
> >
> >
> >
> >
> >
> > > >
> >
> > > ________________________________________________
> >
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> >
> > > ---
> >
> > AutoDock Mailing List - AutoDock<http://autodock.
> scripps.edu/mailing_list>
> >
> > autodock.scripps.edu
> >
> > AutoDock web site
> >
> >
> >
> >
> >
> > >
> >
> > ________________________________________________
> >
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> > AutoDock Mailing List - AutoDock<http://autodock.
> scripps.edu/mailing_list>
> >
> > autodock.scripps.edu
> >
> > AutoDock web site
> >
> >
> >
> >
> >
> > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
> návrhu
> > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> > experimentální botaniky AV ČR, v. v. i.
> >
> >
> >
> > Disclaimer: If not expressly stated otherwise, this e-mail message cannot
> > be considered as a proposal to conclude a contract, neither the
> acceptance
> > of a proposal to conclude a contract, nor does it create any
> > pre-contractual liability on the part of the Institute of experimental
> > botany of the CAS, v. v. i.
> >
> > ________________________________________________
> >
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Hello
can anyone kindly guide me how to prepare small molecule (chemdraw format)
step by step to take it for docking??

On Wed, Nov 15, 2017 at 9:10 AM, Diogo Martins <[hidden email]>
wrote:

> Hello,
>
> Any viewer is OK.
>
> Cheers
>
> On Nov 14, 2017 9:15 PM, "bushra TAJ" <[hidden email]> wrote:
>
> > Hello
> > Is that OK to analyse binding modes and distances using Chimera?? cant we
> > report it as authentic??
> > Is VMD the only options for windows OS??
> > Regards
> >
> > On Tue, Nov 14, 2017 at 3:57 AM, Jakubowski, Henry <
> [hidden email]
> > >
> > wrote:
> >
> > > Hello,
> > >
> > >
> > >
> > > I think what she means is how to analyze a pdb file generated by
> Autodock
> > > vina for intermolecular forces involved in ligand/protein interactions.
> > >
> > >
> > >
> > > Chimera is great for display but I don't think it works very well for
> the
> > > visual analysis of IMFs.  You can choose Tools, Surface Binding
> Analyses,
> > > Find H bonds, for example, but the output is not robust as when you
> used
> > > the PDBs ligand explorer for analyzing PDB files downloaded directly
> from
> > > the PDB.
> > >
> > >
> > >
> > > Ligand Explorer doesn't work (for me anyway) with PDB files derived
> from
> > > Autodock Vina or from those files uploaded first into Chimera, saved
> and
> > > then analyzed by Ligand Explorer.
> > >
> > >
> > >
> > > I have my students use VMD<http://www.ks.uiuc.edu/Research/vmd/> for
> the
> > > analyses of IMFs.  I've pasted the instructions below.  They are a bit
> > > convoluted.
> > >
> > >
> > >
> > >   1.  Load your docked ligand/protein complex into VMD (File, New
> > > Molecule, Browse ..).
> > >   2.  In the VMD Main window select Extensions, TK console.
> > >   3.  To find out what directory you are in, type     ls        (for
> > list)
> > >   4.  Next type    cd ..   (that is cd space dot dot) to change
> > > directories (cd) to the directory above the one you are in at present.
> > > Type   ls   again.
> > >   5.  Repeat cd and ls until when you type  ls you find the folder
> Users/
> > >   6.  Type in cd Users to see the individual user folder (it's case
> > > sensitive)
> > >   7.  Type   ls to see the folders
> > >   8.  Type cd yourusername to move to your folder, and  then ls  is see
> > > what's in your folder..
> > >   9.  [if you are using your own PC, type cd Documents to get to your
> > > document folder or if you can't find that cd Desktop.)  If you are
> using
> > a
> > > networked PC, just stay in your username folder.
> > >   10. Now create a variable (csn) that will store the protein:ligand
> > > structure coordinates by typing the follow:  set csn [atomselect top
> all]
> > >     (this will save protein and ligand coordinates)
> > >   11. Finally type   $csn writepdb csnall.pdb
> > > You should be able to find it in the following folder:
> > > M:\CitrixProfile\UPM_Profile\Downloads.  It might take a few minutes
> for
> > > it to appear however.  It might appear in the Citrix/Pending folder.
> > >
> > > Save the file in one of your regular folders.  Go to Protein Ligand
> > > Interaction Profiler<https://projects.biotec.tu-dresden.de/plip-web/
> > > plip/index>.  Upload your file by browsing to your file.  Submit the
> file
> > > and visualize the results when finished (as illustrated below)
> > > [cid:image003.jpg@01D35D0D.683C32D0]
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > You will see a table detailing the ligand:protein interactions.
> > >
> > >
> > >
> > > Does anyone have a better way to visually analyze the docked
> > > ligand:protein IMFs?  (i.e is there an external program designed
> > > specifically to analyze the IMFs that works on pdb files saved by
> > autodock
> > > vina?
> > >
> > >
> > >
> > > Thanks
> > >
> > > Henry Jakubowski
> > >
> > >
> > > .
> > > Chemistry Department
> > > College of St. Benedict/St. John's University
> > > 37 S. College Ave.
> > > St. Joseph, MN 56374
> > >
> > > e:  [hidden email]<mailto:[hidden email]>
> > > w:  http://employees.csbsju.edu/hjakubowski
> > > Biochemistry Online:  An Approach Based on Chemical Logic<
> > > http://employees.csbsju.edu/hjakubowski/classes/ch331/
> > bcintro/default.html
> > > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > -----Original Message-----
> > > From: [hidden email] [mailto:autodock-bounces@
> scripps.edu]
> > > On Behalf Of Dvoráková Marcela UEB
> > > Sent: Tuesday, November 14, 2017 2:15 AM
> > > To: [hidden email]
> > > Subject: Re: ADL: viewing results
> > >
> > >
> > >
> > > Hi, thanks for the suggestions...
> > >
> > >
> > >
> > > I use pymol, but it shows only polar contacts...I would like to see
> also
> > > the hydrophobic contacts...
> > >
> > >
> > >
> > > I downloaded chimera, but I do not know how to display the vina results
> > > there showing the contacts.
> > >
> > >
> > >
> > >
> > >
> > > ________________________________
> > >
> > > Od: [hidden email]<mailto:[hidden email]>
> <
> > > [hidden email]<mailto:[hidden email]>> za
> > > uživatele Diogo Martins <[hidden email]<mailto:
> > > [hidden email]>>
> > >
> > > Odesláno: pondělí 13. listopadu 2017 20:47
> > >
> > > Komu: [hidden email]<mailto:[hidden email]>
> > >
> > > Předmět: Re: ADL: viewing results
> > >
> > >
> > >
> > > I suggest these two:
> > >
> > >
> > >
> > > pymol: https://sourceforge.net/projects/pymol/
> > >
> > > [https://a.fsdn.com/allura/p/pymol/icon?1491835960]<https:/
> > > /sourceforge.net/projects/pymol/>
> > >
> > >
> > >
> > > PyMOL Molecular Graphics System download | SourceForge.net<https://
> > > sourceforge.net/projects/pymol/>
> > >
> > > sourceforge.net
> > >
> > > Download PyMOL Molecular Graphics System for free. PyMOL is an OpenGL
> > > based molecular visualization system. PyMOL is a Python-enhanced
> > molecular
> > > graphics tool. It excels at 3D visualization of proteins, small
> > molecules,
> > > density, surfaces, and trajectories.
> > >
> > >
> > >
> > >
> > >
> > > pmv (part of MGLTools): http://mgltools.scripps.edu/downloads
> > >
> > >
> > >
> > > On 13 November 2017 at 03:52, bushra TAJ <[hidden email]
> <mailto:
> > > [hidden email]>> wrote:
> > >
> > >
> > >
> > > > Hello
> > >
> > > > I will suggest you to use Chimera it is free available for windows
> and
> > >
> > > > unlimited without any trial period. I am using it myslef.
> > >
> > > >
> > >
> > > > On Mon, Nov 13, 2017 at 3:41 AM, Dvořáková Marcela UEB <
> > >
> > > > [hidden email]<mailto:[hidden email]>
> > >
> > > > > wrote:
> > >
> > > >
> > >
> > > > > Hi,
> > >
> > > > >
> > >
> > > > >
> > >
> > > > > may anyone advise me on how to view te vina results in Ligandscout?
> > >
> > > > > I got through the pdf tutorial but I did not get it. I am using
> just
> > >
> > > > > the free 30-days trial version of Ligandscout.
> > >
> > > > >
> > >
> > > > >
> > >
> > > > > Or may anyone suggest another program (for windows) which would
> > >
> > > > > nicely display the interactions of ligand with protein (polar as
> > >
> > > > > well as hydrophobic)?
> > >
> > > > >
> > >
> > > > >
> > >
> > > > > Thanks, Marcela
> > >
> > > > >
> > >
> > > > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> > >
> > > > > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím
> případného
> > >
> > > > návrhu
> > >
> > > > > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> > >
> > > > > experimentální botaniky AV ČR, v. v. i.
> > >
> > > > >
> > >
> > > > > Disclaimer: If not expressly stated otherwise, this e-mail message
> > >
> > > > > cannot be considered as a proposal to conclude a contract, neither
> > >
> > > > > the
> > >
> > > > acceptance
> > >
> > > > > of a proposal to conclude a contract, nor does it create any
> > >
> > > > > pre-contractual liability on the part of the Institute of
> > >
> > > > > experimental botany of the CAS, v. v. i.
> > >
> > > > > ________________________________________________
> > >
> > > > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/
> mailing_list
> > >
> > > > > ---
> > >
> > > AutoDock Mailing List - AutoDock<http://autodock.
> > scripps.edu/mailing_list>
> > >
> > > autodock.scripps.edu
> > >
> > > AutoDock web site
> > >
> > >
> > >
> > >
> > >
> > > > >
> > >
> > > > ________________________________________________
> > >
> > > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> > >
> > > > ---
> > >
> > > AutoDock Mailing List - AutoDock<http://autodock.
> > scripps.edu/mailing_list>
> > >
> > > autodock.scripps.edu
> > >
> > > AutoDock web site
> > >
> > >
> > >
> > >
> > >
> > > >
> > >
> > > ________________________________________________
> > >
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> > > AutoDock Mailing List - AutoDock<http://autodock.
> > scripps.edu/mailing_list>
> > >
> > > autodock.scripps.edu
> > >
> > > AutoDock web site
> > >
> > >
> > >
> > >
> > >
> > > Upozornění: Není-li v této zprávě výslovně uvedeno jinak, není tato
> > > e-mailová zpráva návrhem na uzavření smlouvy ani přijetím případného
> > návrhu
> > > na uzavření smlouvy a nezakládá předsmluvní odpovědnost Ústavu
> > > experimentální botaniky AV ČR, v. v. i.
> > >
> > >
> > >
> > > Disclaimer: If not expressly stated otherwise, this e-mail message
> cannot
> > > be considered as a proposal to conclude a contract, neither the
> > acceptance
> > > of a proposal to conclude a contract, nor does it create any
> > > pre-contractual liability on the part of the Institute of experimental
> > > botany of the CAS, v. v. i.
> > >
> > > ________________________________________________
> > >
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> > >
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> > >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Roberta King
If you have Chemdraw 3D it is very easy. Just copy the chemdraw structure
into Chem3D, make sure the bonds and ionization are what you want (i.e.,
aromatic ring labeled as all aromatic bonds), then in Calculations menu run
Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
single pass with the default parameters gets to minimum energy and
idealized 3D structure.

The critical issue is to have all the atom types assigned as you want them
(like aromatic carbons and bonds), and hydrogens & charges added as you
want them (O- or OH for example) prior to the minimization.

Saving the minimized structure as .mol2 format should prepare a file
openable in AutodockTools for preparation of .pdbqt files.

Roberta King
Professor of Biomedical and Pharmaceutical Sciences
Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
College of Pharmacy, University of Rhode Island
7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
voice: 401-874-7061; email: [hidden email]

On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]> wrote:

> Hello
> can anyone kindly guide me how to prepare small molecule (chemdraw format)
> step by step to take it for docking??
>
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Thanks for comprehensive responsive. I have just pasted the SMILES in
Corina online tool (it converted this smiles into pdb and mol2 formats). I
used Prodrug (minimization) and Arguslab for energy minimzation and have
taken that file for Autodock (Is that fine??)

On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:

> If you have Chemdraw 3D it is very easy. Just copy the chemdraw structure
> into Chem3D, make sure the bonds and ionization are what you want (i.e.,
> aromatic ring labeled as all aromatic bonds), then in Calculations menu run
> Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
> single pass with the default parameters gets to minimum energy and
> idealized 3D structure.
>
> The critical issue is to have all the atom types assigned as you want them
> (like aromatic carbons and bonds), and hydrogens & charges added as you
> want them (O- or OH for example) prior to the minimization.
>
> Saving the minimized structure as .mol2 format should prepare a file
> openable in AutodockTools for preparation of .pdbqt files.
>
> Roberta King
> Professor of Biomedical and Pharmaceutical Sciences
> Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
> College of Pharmacy, University of Rhode Island
> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> voice: 401-874-7061; email: [hidden email]
>
> On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]> wrote:
>
> > Hello
> > can anyone kindly guide me how to prepare small molecule (chemdraw
> format)
> > step by step to take it for docking??
> >
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Roberta King
I am not familiar with those programs, but if they give a chemically
reasonable 3d structure they should be fine.

On Tue, Nov 21, 2017 at 4:54 PM bushra TAJ <[hidden email]> wrote:

> Thanks for comprehensive responsive. I have just pasted the SMILES in
> Corina online tool (it converted this smiles into pdb and mol2 formats). I
> used Prodrug (minimization) and Arguslab for energy minimzation and have
> taken that file for Autodock (Is that fine??)
>
> On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:
>
> > If you have Chemdraw 3D it is very easy. Just copy the chemdraw structure
> > into Chem3D, make sure the bonds and ionization are what you want (i.e.,
> > aromatic ring labeled as all aromatic bonds), then in Calculations menu
> run
> > Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
> > single pass with the default parameters gets to minimum energy and
> > idealized 3D structure.
> >
> > The critical issue is to have all the atom types assigned as you want
> them
> > (like aromatic carbons and bonds), and hydrogens & charges added as you
> > want them (O- or OH for example) prior to the minimization.
> >
> > Saving the minimized structure as .mol2 format should prepare a file
> > openable in AutodockTools for preparation of .pdbqt files.
> >
> > Roberta King
> > Professor of Biomedical and Pharmaceutical Sciences
> > Academic Advisor, and Director of BS Pharmaceutical Sciences degree
> program
> > College of Pharmacy, University of Rhode Island
> > 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> > voice: 401-874-7061; email: [hidden email]
> >
> > On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]>
> wrote:
> >
> > > Hello
> > > can anyone kindly guide me how to prepare small molecule (chemdraw
> > format)
> > > step by step to take it for docking??
> > >
> > >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
--
Roberta King
Professor of Biomedical and Pharmaceutical Sciences
Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
College of Pharmacy, University of Rhode Island
7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
voice: 401-874-7061; email: [hidden email]
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Thanks for your time.
Regards

On Tue, Nov 21, 2017 at 1:58 PM, Roberta King <[hidden email]> wrote:

> I am not familiar with those programs, but if they give a chemically
> reasonable 3d structure they should be fine.
>
> On Tue, Nov 21, 2017 at 4:54 PM bushra TAJ <[hidden email]> wrote:
>
> > Thanks for comprehensive responsive. I have just pasted the SMILES in
> > Corina online tool (it converted this smiles into pdb and mol2 formats).
> I
> > used Prodrug (minimization) and Arguslab for energy minimzation and have
> > taken that file for Autodock (Is that fine??)
> >
> > On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:
> >
> > > If you have Chemdraw 3D it is very easy. Just copy the chemdraw
> structure
> > > into Chem3D, make sure the bonds and ionization are what you want
> (i.e.,
> > > aromatic ring labeled as all aromatic bonds), then in Calculations menu
> > run
> > > Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
> > > single pass with the default parameters gets to minimum energy and
> > > idealized 3D structure.
> > >
> > > The critical issue is to have all the atom types assigned as you want
> > them
> > > (like aromatic carbons and bonds), and hydrogens & charges added as you
> > > want them (O- or OH for example) prior to the minimization.
> > >
> > > Saving the minimized structure as .mol2 format should prepare a file
> > > openable in AutodockTools for preparation of .pdbqt files.
> > >
> > > Roberta King
> > > Professor of Biomedical and Pharmaceutical Sciences
> > > Academic Advisor, and Director of BS Pharmaceutical Sciences degree
> > program
> > > College of Pharmacy, University of Rhode Island
> > > 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> > > voice: 401-874-7061; email: [hidden email]
> > >
> > > On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]>
> > wrote:
> > >
> > > > Hello
> > > > can anyone kindly guide me how to prepare small molecule (chemdraw
> > > format)
> > > > step by step to take it for docking??
> > > >
> > > >
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> > >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> --
> Roberta King
> Professor of Biomedical and Pharmaceutical Sciences
> Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
> College of Pharmacy, University of Rhode Island
> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> voice: 401-874-7061; email: [hidden email]
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Hello One more query,
if I have made pdb format of small molecule using some online tool and all
this energy minimization, charges and adding hydrogen followed by making
pdbqt from Autodock and then proceed to docking using Autodock tool Don't
you think it will be equally well ??
Instead using chem3D or etc
Need your expert advice

On Tue, Nov 21, 2017 at 2:00 PM, bushra TAJ <[hidden email]> wrote:

> Thanks for your time.
> Regards
>
> On Tue, Nov 21, 2017 at 1:58 PM, Roberta King <[hidden email]> wrote:
>
>> I am not familiar with those programs, but if they give a chemically
>> reasonable 3d structure they should be fine.
>>
>> On Tue, Nov 21, 2017 at 4:54 PM bushra TAJ <[hidden email]> wrote:
>>
>> > Thanks for comprehensive responsive. I have just pasted the SMILES in
>> > Corina online tool (it converted this smiles into pdb and mol2
>> formats). I
>> > used Prodrug (minimization) and Arguslab for energy minimzation and have
>> > taken that file for Autodock (Is that fine??)
>> >
>> > On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:
>> >
>> > > If you have Chemdraw 3D it is very easy. Just copy the chemdraw
>> structure
>> > > into Chem3D, make sure the bonds and ionization are what you want
>> (i.e.,
>> > > aromatic ring labeled as all aromatic bonds), then in Calculations
>> menu
>> > run
>> > > Minimize Energy. This optimizes the bond lengths, angles etc. Usually
>> a
>> > > single pass with the default parameters gets to minimum energy and
>> > > idealized 3D structure.
>> > >
>> > > The critical issue is to have all the atom types assigned as you want
>> > them
>> > > (like aromatic carbons and bonds), and hydrogens & charges added as
>> you
>> > > want them (O- or OH for example) prior to the minimization.
>> > >
>> > > Saving the minimized structure as .mol2 format should prepare a file
>> > > openable in AutodockTools for preparation of .pdbqt files.
>> > >
>> > > Roberta King
>> > > Professor of Biomedical and Pharmaceutical Sciences
>> > > Academic Advisor, and Director of BS Pharmaceutical Sciences degree
>> > program
>> > > College of Pharmacy, University of Rhode Island
>> > > 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
>> > > voice: 401-874-7061; email: [hidden email]
>> > >
>> > > On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]>
>> > wrote:
>> > >
>> > > > Hello
>> > > > can anyone kindly guide me how to prepare small molecule (chemdraw
>> > > format)
>> > > > step by step to take it for docking??
>> > > >
>> > > >
>> > > ________________________________________________
>> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>> ---
>> > >
>> > ________________________________________________
>> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>> ---
>> >
>> --
>> Roberta King
>> Professor of Biomedical and Pharmaceutical Sciences
>> Academic Advisor, and Director of BS Pharmaceutical Sciences degree
>> program
>> College of Pharmacy, University of Rhode Island
>> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
>> voice: 401-874-7061; email: [hidden email]
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Roberta King
Autodock adds partial charges and hydrogens (autodocktools) and rotates
rotatable bonds, but does not adjust any other bond angles or bond lengths.
Whether energy minimization is necessary depends on whether the ligand
structure is already in a realistic state from the source.

On Thu, Nov 23, 2017 at 2:08 AM bushra TAJ <[hidden email]> wrote:

> Hello One more query,
> if I have made pdb format of small molecule using some online tool and all
> this energy minimization, charges and adding hydrogen followed by making
> pdbqt from Autodock and then proceed to docking using Autodock tool Don't
> you think it will be equally well ??
> Instead using chem3D or etc
> Need your expert advice
>
> On Tue, Nov 21, 2017 at 2:00 PM, bushra TAJ <[hidden email]> wrote:
>
> > Thanks for your time.
> > Regards
> >
> > On Tue, Nov 21, 2017 at 1:58 PM, Roberta King <[hidden email]> wrote:
> >
> >> I am not familiar with those programs, but if they give a chemically
> >> reasonable 3d structure they should be fine.
> >>
> >> On Tue, Nov 21, 2017 at 4:54 PM bushra TAJ <[hidden email]>
> wrote:
> >>
> >> > Thanks for comprehensive responsive. I have just pasted the SMILES in
> >> > Corina online tool (it converted this smiles into pdb and mol2
> >> formats). I
> >> > used Prodrug (minimization) and Arguslab for energy minimzation and
> have
> >> > taken that file for Autodock (Is that fine??)
> >> >
> >> > On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:
> >> >
> >> > > If you have Chemdraw 3D it is very easy. Just copy the chemdraw
> >> structure
> >> > > into Chem3D, make sure the bonds and ionization are what you want
> >> (i.e.,
> >> > > aromatic ring labeled as all aromatic bonds), then in Calculations
> >> menu
> >> > run
> >> > > Minimize Energy. This optimizes the bond lengths, angles etc.
> Usually
> >> a
> >> > > single pass with the default parameters gets to minimum energy and
> >> > > idealized 3D structure.
> >> > >
> >> > > The critical issue is to have all the atom types assigned as you
> want
> >> > them
> >> > > (like aromatic carbons and bonds), and hydrogens & charges added as
> >> you
> >> > > want them (O- or OH for example) prior to the minimization.
> >> > >
> >> > > Saving the minimized structure as .mol2 format should prepare a file
> >> > > openable in AutodockTools for preparation of .pdbqt files.
> >> > >
> >> > > Roberta King
> >> > > Professor of Biomedical and Pharmaceutical Sc
> <https://maps.google.com/?q=Professor+of+Biomedical+and+Pharmaceutical+Sc&entry=gmail&source=g>
> iences
> >> > > Academic Advisor, and Director of BS Pharmaceutical Sciences degree
> >> > program
> >> > > College of Pharmacy, University of Rhode Island
> >> > > 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> >> > > voice: 401-874-7061; email: [hidden email]
> >> > >
> >> > > On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]>
> >> > wrote:
> >> > >
> >> > > > Hello
> >> > > > can anyone kindly guide me how to prepare small molecule (chemdraw
> >> > > format)
> >> > > > step by step to take it for docking??
> >> > > >
> >> > > >
> >> > > ________________________________________________
> >> > > --- ADL: AutoDock List  ---
> http://autodock.scripps.edu/mailing_list
> >> ---
> >> > >
> >> > ________________________________________________
> >> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> >> ---
> >> >
> >> --
> >> Roberta King
> >> Professor of Biomedical and Pharmaceutical Sciences
> >> Academic Advisor, and Director of BS Pharmaceutical Sciences degree
> >> program
> >> College of Pharmacy, University of Rhode Island
> >> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> >> voice: 401-874-7061; email: [hidden email]
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> >>
> >
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
--
Roberta King
Professor of Biomedical and Pharmaceutical Sciences
Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
College of Pharmacy, University of Rhode Island
7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
voice: 401-874-7061; email: [hidden email]
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
hmm Yes you are right, but if structure is just recently synthesized small
molecule and I have just got the chem draw structure and have made Pdb
using Corina online tool. In that case you will not suggest Autodock alone
??

On Thu, Nov 23, 2017 at 6:42 AM, Roberta King <[hidden email]> wrote:

> Autodock adds partial charges and hydrogens (autodocktools) and rotates
> rotatable bonds, but does not adjust any other bond angles or bond lengths.
> Whether energy minimization is necessary depends on whether the ligand
> structure is already in a realistic state from the source.
>
> On Thu, Nov 23, 2017 at 2:08 AM bushra TAJ <[hidden email]> wrote:
>
> > Hello One more query,
> > if I have made pdb format of small molecule using some online tool and
> all
> > this energy minimization, charges and adding hydrogen followed by making
> > pdbqt from Autodock and then proceed to docking using Autodock tool Don't
> > you think it will be equally well ??
> > Instead using chem3D or etc
> > Need your expert advice
> >
> > On Tue, Nov 21, 2017 at 2:00 PM, bushra TAJ <[hidden email]>
> wrote:
> >
> > > Thanks for your time.
> > > Regards
> > >
> > > On Tue, Nov 21, 2017 at 1:58 PM, Roberta King <[hidden email]> wrote:
> > >
> > >> I am not familiar with those programs, but if they give a chemically
> > >> reasonable 3d structure they should be fine.
> > >>
> > >> On Tue, Nov 21, 2017 at 4:54 PM bushra TAJ <[hidden email]>
> > wrote:
> > >>
> > >> > Thanks for comprehensive responsive. I have just pasted the SMILES
> in
> > >> > Corina online tool (it converted this smiles into pdb and mol2
> > >> formats). I
> > >> > used Prodrug (minimization) and Arguslab for energy minimzation and
> > have
> > >> > taken that file for Autodock (Is that fine??)
> > >> >
> > >> > On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]>
> wrote:
> > >> >
> > >> > > If you have Chemdraw 3D it is very easy. Just copy the chemdraw
> > >> structure
> > >> > > into Chem3D, make sure the bonds and ionization are what you want
> > >> (i.e.,
> > >> > > aromatic ring labeled as all aromatic bonds), then in Calculations
> > >> menu
> > >> > run
> > >> > > Minimize Energy. This optimizes the bond lengths, angles etc.
> > Usually
> > >> a
> > >> > > single pass with the default parameters gets to minimum energy and
> > >> > > idealized 3D structure.
> > >> > >
> > >> > > The critical issue is to have all the atom types assigned as you
> > want
> > >> > them
> > >> > > (like aromatic carbons and bonds), and hydrogens & charges added
> as
> > >> you
> > >> > > want them (O- or OH for example) prior to the minimization.
> > >> > >
> > >> > > Saving the minimized structure as .mol2 format should prepare a
> file
> > >> > > openable in AutodockTools for preparation of .pdbqt files.
> > >> > >
> > >> > > Roberta King
> > >> > > Professor of Biomedical and Pharmaceutical Sc
> > <https://maps.google.com/?q=Professor+of+Biomedical+and+
> Pharmaceutical+Sc&entry=gmail&source=g>
> > iences
> > >> > > Academic Advisor, and Director of BS Pharmaceutical Sciences
> degree
> > >> > program
> > >> > > College of Pharmacy, University of Rhode Island
> > >> > > 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> > >> > > voice: 401-874-7061; email: [hidden email]
> > >> > >
> > >> > > On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <
> [hidden email]>
> > >> > wrote:
> > >> > >
> > >> > > > Hello
> > >> > > > can anyone kindly guide me how to prepare small molecule
> (chemdraw
> > >> > > format)
> > >> > > > step by step to take it for docking??
> > >> > > >
> > >> > > >
> > >> > > ________________________________________________
> > >> > > --- ADL: AutoDock List  ---
> > http://autodock.scripps.edu/mailing_list
> > >> ---
> > >> > >
> > >> > ________________________________________________
> > >> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/
> mailing_list
> > >> ---
> > >> >
> > >> --
> > >> Roberta King
> > >> Professor of Biomedical and Pharmaceutical Sciences
> > >> Academic Advisor, and Director of BS Pharmaceutical Sciences degree
> > >> program
> > >> College of Pharmacy, University of Rhode Island
> > >> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> > >> voice: 401-874-7061; email: [hidden email]
> > >> ________________________________________________
> > >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> > ---
> > >>
> > >
> > >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> --
> Roberta King
> Professor of Biomedical and Pharmaceutical Sciences
> Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
> College of Pharmacy, University of Rhode Island
> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> voice: 401-874-7061; email: [hidden email]
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
In reply to this post by Roberta King
If have lone pair in ligand and MMF in Chem3d do not work on such molecule
is it fine to stick to energy minimization step of MM2 in Chem3d?

On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:

> If you have Chemdraw 3D it is very easy. Just copy the chemdraw structure
> into Chem3D, make sure the bonds and ionization are what you want (i.e.,
> aromatic ring labeled as all aromatic bonds), then in Calculations menu run
> Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
> single pass with the default parameters gets to minimum energy and
> idealized 3D structure.
>
> The critical issue is to have all the atom types assigned as you want them
> (like aromatic carbons and bonds), and hydrogens & charges added as you
> want them (O- or OH for example) prior to the minimization.
>
> Saving the minimized structure as .mol2 format should prepare a file
> openable in AutodockTools for preparation of .pdbqt files.
>
> Roberta King
> Professor of Biomedical and Pharmaceutical Sciences
> Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
> College of Pharmacy, University of Rhode Island
> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> voice: 401-874-7061; email: [hidden email]
>
> On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]> wrote:
>
> > Hello
> > can anyone kindly guide me how to prepare small molecule (chemdraw
> format)
> > step by step to take it for docking??
> >
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
In reply to this post by Roberta King
Dynamics terminated because the molecular model is too far from equilibrium

what does that mean and how to fix it in Chem3D??

On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:

> If you have Chemdraw 3D it is very easy. Just copy the chemdraw structure
> into Chem3D, make sure the bonds and ionization are what you want (i.e.,
> aromatic ring labeled as all aromatic bonds), then in Calculations menu run
> Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
> single pass with the default parameters gets to minimum energy and
> idealized 3D structure.
>
> The critical issue is to have all the atom types assigned as you want them
> (like aromatic carbons and bonds), and hydrogens & charges added as you
> want them (O- or OH for example) prior to the minimization.
>
> Saving the minimized structure as .mol2 format should prepare a file
> openable in AutodockTools for preparation of .pdbqt files.
>
> Roberta King
> Professor of Biomedical and Pharmaceutical Sciences
> Academic Advisor, and Director of BS Pharmaceutical Sciences degree program
> College of Pharmacy, University of Rhode Island
> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> voice: 401-874-7061; email: [hidden email]
>
> On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]> wrote:
>
> > Hello
> > can anyone kindly guide me how to prepare small molecule (chemdraw
> format)
> > step by step to take it for docking??
> >
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

bushra TAJ
Hello
I am using Chem3D for energy minimization of my small molecules. Every time
I am calculating charges this messege appears:
*"there was an error computing the huckel charges for this model"*

*Can anyone guide me how to fix this??*
Although when I run MM2 energy minimization without this step it proceeds
very well.

On Thu, Nov 23, 2017 at 8:59 AM, bushra TAJ <[hidden email]> wrote:

> Dynamics terminated because the molecular model is too far from equilibrium
>
> what does that mean and how to fix it in Chem3D??
>
> On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:
>
>> If you have Chemdraw 3D it is very easy. Just copy the chemdraw structure
>> into Chem3D, make sure the bonds and ionization are what you want (i.e.,
>> aromatic ring labeled as all aromatic bonds), then in Calculations menu
>> run
>> Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
>> single pass with the default parameters gets to minimum energy and
>> idealized 3D structure.
>>
>> The critical issue is to have all the atom types assigned as you want them
>> (like aromatic carbons and bonds), and hydrogens & charges added as you
>> want them (O- or OH for example) prior to the minimization.
>>
>> Saving the minimized structure as .mol2 format should prepare a file
>> openable in AutodockTools for preparation of .pdbqt files.
>>
>> Roberta King
>> Professor of Biomedical and Pharmaceutical Sciences
>> Academic Advisor, and Director of BS Pharmaceutical Sciences degree
>> program
>> College of Pharmacy, University of Rhode Island
>> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
>> voice: 401-874-7061; email: [hidden email]
>>
>> On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]>
>> wrote:
>>
>> > Hello
>> > can anyone kindly guide me how to prepare small molecule (chemdraw
>> format)
>> > step by step to take it for docking??
>> >
>> >
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
Reply | Threaded
Open this post in threaded view
|

Re: ADL: viewing results

Dr. M. Shahid
Hi,

btw this is not a mailing list regarding chem3d etc. there might be a
relevant mailing list regarding chem3d suites...

in my opinion, it means your input molecule has some geometry problems or
the forcefield used is not working in the MM step.
if you draw a molecule, you should generate its protomers/tautomeric states
at physiological pH ranges and then do minimizations by using force fields
suitable for small molecules.
then you can try to dock the different states of the ligand...

Best regards,

--
Shahid.


On Fri, Nov 24, 2017 at 9:22 AM, bushra TAJ <[hidden email]> wrote:

> Hello
> I am using Chem3D for energy minimization of my small molecules. Every time
> I am calculating charges this messege appears:
> *"there was an error computing the huckel charges for this model"*
>
> *Can anyone guide me how to fix this??*
> Although when I run MM2 energy minimization without this step it proceeds
> very well.
>
> On Thu, Nov 23, 2017 at 8:59 AM, bushra TAJ <[hidden email]> wrote:
>
> > Dynamics terminated because the molecular model is too far from
> equilibrium
> >
> > what does that mean and how to fix it in Chem3D??
> >
> > On Tue, Nov 21, 2017 at 1:48 PM, Roberta King <[hidden email]> wrote:
> >
> >> If you have Chemdraw 3D it is very easy. Just copy the chemdraw
> structure
> >> into Chem3D, make sure the bonds and ionization are what you want (i.e.,
> >> aromatic ring labeled as all aromatic bonds), then in Calculations menu
> >> run
> >> Minimize Energy. This optimizes the bond lengths, angles etc. Usually a
> >> single pass with the default parameters gets to minimum energy and
> >> idealized 3D structure.
> >>
> >> The critical issue is to have all the atom types assigned as you want
> them
> >> (like aromatic carbons and bonds), and hydrogens & charges added as you
> >> want them (O- or OH for example) prior to the minimization.
> >>
> >> Saving the minimized structure as .mol2 format should prepare a file
> >> openable in AutodockTools for preparation of .pdbqt files.
> >>
> >> Roberta King
> >> Professor of Biomedical and Pharmaceutical Sciences
> >> Academic Advisor, and Director of BS Pharmaceutical Sciences degree
> >> program
> >> College of Pharmacy, University of Rhode Island
> >> 7 Greenhouse Rd, Kingston RI 02881, Room 495L and 470.
> >> voice: 401-874-7061; email: [hidden email]
> >>
> >> On Tue, Nov 21, 2017 at 3:01 PM, bushra TAJ <[hidden email]>
> >> wrote:
> >>
> >> > Hello
> >> > can anyone kindly guide me how to prepare small molecule (chemdraw
> >> format)
> >> > step by step to take it for docking??
> >> >
> >> >
> >> ________________________________________________
> >> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> >>
> >
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
12