ADL: display of Vina results

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ADL: display of Vina results

Dvořáková Marcela UEB
Hi,


I am using Autodock Vina to dock nitrogen-containing molecules. However, when I open the results in Pymol, there are just asterixes where the nitrogen atoms should be and the bonds towards these atoms are missing. I create the molecules in ChemSketch, use "Optimise for 3D" and safe as mol file. I the open the mol file in Pymol and safe as pdb. Then I open the pdb file in Autodock tools (through: Ligand - Input - Open) and safe as pdbqt. Until here the molecule looks fine. Then I run Autodock Vina and when I open the results in Pymol, the structure is demaged.


I also tried to open the results in Autodock tools. There, the structure appears normal, but when I add macromolecule and use Analyze - docking - show interaction, an error massage appears:


Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autoanalyzeCommands.py", line 3087, in doit
    self.build()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build
    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py", line 49, in __init__
    self.build(detect_pi=detect_pi)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py", line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py", line 69, in buildCloseContactAtoms
    self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py", line 106, in select
    bigC = Numeric.resize(c, (lenC, lenC, 3))
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py", line 615, in resize
    a = concatenate( (a,)*n_copies)
MemoryError


May you have an idea what is wrong?


Best regards,

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 ---
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Re: ADL: display of Vina results

Diogo Martins
Hi,

It's hard to figure out the problem without looking at the input ligand. It
could be a problem with the torsion tree. Do all branch/endbranch keywords
look ok?

Best,


On Aug 14, 2017 6:29 AM, "Dvořáková Marcela UEB" <[hidden email]>
wrote:

Hi,


I am using Autodock Vina to dock nitrogen-containing molecules. However,
when I open the results in Pymol, there are just asterixes where the
nitrogen atoms should be and the bonds towards these atoms are missing. I
create the molecules in ChemSketch, use "Optimise for 3D" and safe as mol
file. I the open the mol file in Pymol and safe as pdb. Then I open the pdb
file in Autodock tools (through: Ligand - Input - Open) and safe as pdbqt.
Until here the molecule looks fine. Then I run Autodock Vina and when I
open the results in Pymol, the structure is demaged.


I also tried to open the results in Autodock tools. There, the structure
appears normal, but when I add macromolecule and use Analyze - docking -
show interaction, an error massage appears:


Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-
packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-
packages\AutoDockTools\autoanalyzeCommands.py", line 3087, in doit
    self.build()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-
packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build
    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 49, in __init__
    self.build(detect_pi=detect_pi)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 69, in buildCloseContactAtoms
    self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py",
line 106, in select
    bigC = Numeric.resize(c, (lenC, lenC, 3))
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py",
line 615, in resize
    a = concatenate( (a,)*n_copies)
MemoryError


May you have an idea what is wrong?


Best regards,

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 ---
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Re: ADL: display of Vina results

Dvořáková Marcela UEB
Hi,

to be honest, I have no idea where to find branch/endbranch keywords and how they should look like (I woudnt recognise if they are wrong). I only input ligand, choose torsions, which seem Ok and then output the ligand as pdbqt. When I open this pdbqt file in Pymol (even before running vina), the structure is already demaged.


I also tried different chemical drawing softwares which did not help, tried to copy SMARTs from chemdraw to pdb-converting softwares to avoid pymol (after that it looked even worse - when I use pymol the asterixes appear only at N which are part of a cycle (like pyrimidine) while by copying smarts all nitrogens where just asterixes without bonds).


Compound in pymol:


[cid:10deeb67-994f-4ef6-8e7a-8cf5ef7c3bf0]


Cheers, Marcela

________________________________
Od: [hidden email] <[hidden email]> za uživatele Diogo Martins <[hidden email]>
Odesláno: pondělí 14. srpna 2017 18:17
Komu: [hidden email]
Předmět: Re: ADL: display of Vina results

Hi,

It's hard to figure out the problem without looking at the input ligand. It
could be a problem with the torsion tree. Do all branch/endbranch keywords
look ok?

Best,


On Aug 14, 2017 6:29 AM, "Dvořáková Marcela UEB" <[hidden email]>
wrote:

Hi,


I am using Autodock Vina to dock nitrogen-containing molecules. However,
when I open the results in Pymol, there are just asterixes where the
nitrogen atoms should be and the bonds towards these atoms are missing. I
create the molecules in ChemSketch, use "Optimise for 3D" and safe as mol
file. I the open the mol file in Pymol and safe as pdb. Then I open the pdb
file in Autodock tools (through: Ligand - Input - Open) and safe as pdbqt.
Until here the molecule looks fine. Then I run Autodock Vina and when I
open the results in Pymol, the structure is demaged.


I also tried to open the results in Autodock tools. There, the structure
appears normal, but when I add macromolecule and use Analyze - docking -
show interaction, an error massage appears:


Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-
packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-
packages\AutoDockTools\autoanalyzeCommands.py", line 3087, in doit
    self.build()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site-
packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build
    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 49, in __init__
    self.build(detect_pi=detect_pi)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 69, in buildCloseContactAtoms
    self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py",
line 106, in select
    bigC = Numeric.resize(c, (lenC, lenC, 3))
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py",
line 615, in resize
    a = concatenate( (a,)*n_copies)
MemoryError


May you have an idea what is wrong?


Best regards,

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


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 ---
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Re: ADL: display of Vina results

Bennion, Brian
Why not just use chemdraw to save the structure as a pdb file?  You can even minimize its structure in chemdraw before saving it.

Brian


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Dvoráková Marcela UEB
Sent: Tuesday, August 15, 2017 08:30
To: [hidden email]
Subject: Re: ADL: display of Vina results

Hi,

to be honest, I have no idea where to find branch/endbranch keywords and how they should look like (I woudnt recognise if they are wrong). I only input ligand, choose torsions, which seem Ok and then output the ligand as pdbqt. When I open this pdbqt file in Pymol (even before running vina), the structure is already demaged.


I also tried different chemical drawing softwares which did not help, tried to copy SMARTs from chemdraw to pdb-converting softwares to avoid pymol (after that it looked even worse - when I use pymol the asterixes appear only at N which are part of a cycle (like pyrimidine) while by copying smarts all nitrogens where just asterixes without bonds).


Compound in pymol:


[cid:10deeb67-994f-4ef6-8e7a-8cf5ef7c3bf0]


Cheers, Marcela

________________________________
Od: [hidden email] <[hidden email]> za uživatele Diogo Martins <[hidden email]>
Odesláno: pondělí 14. srpna 2017 18:17
Komu: [hidden email]
Předmět: Re: ADL: display of Vina results

Hi,

It's hard to figure out the problem without looking at the input ligand. It could be a problem with the torsion tree. Do all branch/endbranch keywords look ok?

Best,


On Aug 14, 2017 6:29 AM, "Dvořáková Marcela UEB" <[hidden email]>
wrote:

Hi,


I am using Autodock Vina to dock nitrogen-containing molecules. However, when I open the results in Pymol, there are just asterixes where the nitrogen atoms should be and the bonds towards these atoms are missing. I create the molecules in ChemSketch, use "Optimise for 3D" and safe as mol file. I the open the mol file in Pymol and safe as pdb. Then I open the pdb file in Autodock tools (through: Ligand - Input - Open) and safe as pdbqt.
Until here the molecule looks fine. Then I run Autodock Vina and when I open the results in Pymol, the structure is demaged.


I also tried to open the results in Autodock tools. There, the structure appears normal, but when I add macromolecule and use Analyze - docking - show interaction, an error massage appears:


Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 3087, in doit
    self.build()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build
    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 49, in __init__
    self.build(detect_pi=detect_pi)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 69, in buildCloseContactAtoms
    self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py",
line 106, in select
    bigC = Numeric.resize(c, (lenC, lenC, 3))
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py",
line 615, in resize
    a = concatenate( (a,)*n_copies)
MemoryError


May you have an idea what is wrong?


Best regards,

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


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 ---
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Re: ADL: display of Vina results

Dvořáková Marcela UEB
I did not know this is possible, I know I can save it as mol file in chemdraw. Also, I dont know how to optimize 3D structure in chemdraw, I tried: Edit - Get 3D Model and saved it as mol file, then i converted it to pdb in pymol, but when I opened it in autodock tools the structure does not look like chemical structure at all...

[cid:58e288a0-9e1a-4b24-ac47-7e1ba30ceb58]

________________________________
Od: [hidden email] <[hidden email]> za uživatele Bennion, Brian <[hidden email]>
Odesláno: úterý 15. srpna 2017 17:36
Komu: [hidden email]
Předmět: Re: ADL: display of Vina results

Why not just use chemdraw to save the structure as a pdb file?  You can even minimize its structure in chemdraw before saving it.

Brian


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Dvoráková Marcela UEB
Sent: Tuesday, August 15, 2017 08:30
To: [hidden email]
Subject: Re: ADL: display of Vina results

Hi,

to be honest, I have no idea where to find branch/endbranch keywords and how they should look like (I woudnt recognise if they are wrong). I only input ligand, choose torsions, which seem Ok and then output the ligand as pdbqt. When I open this pdbqt file in Pymol (even before running vina), the structure is already demaged.


I also tried different chemical drawing softwares which did not help, tried to copy SMARTs from chemdraw to pdb-converting softwares to avoid pymol (after that it looked even worse - when I use pymol the asterixes appear only at N which are part of a cycle (like pyrimidine) while by copying smarts all nitrogens where just asterixes without bonds).


Compound in pymol:


[cid:10deeb67-994f-4ef6-8e7a-8cf5ef7c3bf0]


Cheers, Marcela

________________________________
Od: [hidden email] <[hidden email]> za uživatele Diogo Martins <[hidden email]>
Odesláno: pondělí 14. srpna 2017 18:17
Komu: [hidden email]
Předmět: Re: ADL: display of Vina results

Hi,

It's hard to figure out the problem without looking at the input ligand. It could be a problem with the torsion tree. Do all branch/endbranch keywords look ok?

Best,


On Aug 14, 2017 6:29 AM, "Dvořáková Marcela UEB" <[hidden email]>
wrote:

Hi,


I am using Autodock Vina to dock nitrogen-containing molecules. However, when I open the results in Pymol, there are just asterixes where the nitrogen atoms should be and the bonds towards these atoms are missing. I create the molecules in ChemSketch, use "Optimise for 3D" and safe as mol file. I the open the mol file in Pymol and safe as pdb. Then I open the pdb file in Autodock tools (through: Ligand - Input - Open) and safe as pdbqt.
Until here the molecule looks fine. Then I run Autodock Vina and when I open the results in Pymol, the structure is demaged.


I also tried to open the results in Autodock tools. There, the structure appears normal, but when I add macromolecule and use Analyze - docking - show interaction, an error massage appears:


Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 3087, in doit
    self.build()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build
    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 49, in __init__
    self.build(detect_pi=detect_pi)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 69, in buildCloseContactAtoms
    self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py",
line 106, in select
    bigC = Numeric.resize(c, (lenC, lenC, 3))
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py",
line 615, in resize
    a = concatenate( (a,)*n_copies)
MemoryError


May you have an idea what is wrong?


Best regards,

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.

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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.

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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.

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Re: ADL: display of Vina results

Bennion, Brian
You just need to select another output format before you save your molecule.  It will complain that you are loosing lots of information, but that is happening anyway with the mol file.  

There is also Avogadro which does a decent job with many small molecule formats.  It is public domain and available for mac, linux, and windows.

I can talk a look at the ligand if you want, just post it off list.
Brian


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Dvoráková Marcela UEB
Sent: Tuesday, August 15, 2017 08:56
To: [hidden email]
Subject: Re: ADL: display of Vina results

I did not know this is possible, I know I can save it as mol file in chemdraw. Also, I dont know how to optimize 3D structure in chemdraw, I tried: Edit - Get 3D Model and saved it as mol file, then i converted it to pdb in pymol, but when I opened it in autodock tools the structure does not look like chemical structure at all...

[cid:58e288a0-9e1a-4b24-ac47-7e1ba30ceb58]

________________________________
Od: [hidden email] <[hidden email]> za uživatele Bennion, Brian <[hidden email]>
Odesláno: úterý 15. srpna 2017 17:36
Komu: [hidden email]
Předmět: Re: ADL: display of Vina results

Why not just use chemdraw to save the structure as a pdb file?  You can even minimize its structure in chemdraw before saving it.

Brian


-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Dvoráková Marcela UEB
Sent: Tuesday, August 15, 2017 08:30
To: [hidden email]
Subject: Re: ADL: display of Vina results

Hi,

to be honest, I have no idea where to find branch/endbranch keywords and how they should look like (I woudnt recognise if they are wrong). I only input ligand, choose torsions, which seem Ok and then output the ligand as pdbqt. When I open this pdbqt file in Pymol (even before running vina), the structure is already demaged.


I also tried different chemical drawing softwares which did not help, tried to copy SMARTs from chemdraw to pdb-converting softwares to avoid pymol (after that it looked even worse - when I use pymol the asterixes appear only at N which are part of a cycle (like pyrimidine) while by copying smarts all nitrogens where just asterixes without bonds).


Compound in pymol:


[cid:10deeb67-994f-4ef6-8e7a-8cf5ef7c3bf0]


Cheers, Marcela

________________________________
Od: [hidden email] <[hidden email]> za uživatele Diogo Martins <[hidden email]>
Odesláno: pondělí 14. srpna 2017 18:17
Komu: [hidden email]
Předmět: Re: ADL: display of Vina results

Hi,

It's hard to figure out the problem without looking at the input ligand. It could be a problem with the torsion tree. Do all branch/endbranch keywords look ok?

Best,


On Aug 14, 2017 6:29 AM, "Dvořáková Marcela UEB" <[hidden email]>
wrote:

Hi,


I am using Autodock Vina to dock nitrogen-containing molecules. However, when I open the results in Pymol, there are just asterixes where the nitrogen atoms should be and the bonds towards these atoms are missing. I create the molecules in ChemSketch, use "Optimise for 3D" and safe as mol file. I the open the mol file in Pymol and safe as pdb. Then I open the pdb file in Autodock tools (through: Ligand - Input - Open) and safe as pdbqt.
Until here the molecule looks fine. Then I run Autodock Vina and when I open the results in Pymol, the structure is demaged.


I also tried to open the results in Autodock tools. There, the structure appears normal, but when I add macromolecule and use Analyze - docking - show interaction, an error massage appears:


Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
Unable to assign HYB type to atom N
ERROR *********************************************
Traceback (most recent call last):
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\ViewerFramework\VF.py", line 898, in tryto
    result = command( *args, **kw )
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 3087, in doit
    self.build()
  File "C:\Program Files (x86)\MGLTools-1.5.6\lib\site- packages\AutoDockTools\autoanalyzeCommands.py", line 2912, in build
    self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 49, in __init__
    self.build(detect_pi=detect_pi)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 60, in build
    self.buildCloseContactAtoms(percentCutoff)              #
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\interactionDescriptor.py",
line 69, in buildCloseContactAtoms
    self.macro_atoms, percentCutoff=percentCutoff)
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\MolKit\distanceSelector.py",
line 106, in select
    bigC = Numeric.resize(c, (lenC, lenC, 3))
  File "C:\Program Files
(x86)\MGLTools-1.5.6\lib\site-packages\numpy\core\fromnumeric.py",
line 615, in resize
    a = concatenate( (a,)*n_copies)
MemoryError


May you have an idea what is wrong?


Best regards,

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.
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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.

________________________________________________
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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.

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