ADL: about PDB file

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ADL: about PDB file

Qinghua Liao
Dear sirs,


After docking using autodock4, I saved the conformation of ligand in PDB file, but the  PDB file format had some problems, it's not correct. And when I used ligplot to detect the interaction between ligand and receptor, it could not detect the existence of the ligand because the problem of PDB format. So my question is how can I get the correct PDB format after docking using autodock4? Thanks very much!


All the best!

Qinghua



     
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Re: ADL: about PDB file

Davide Mercadante
Hi Qinghua,

I don't understand sorry. How you can get the docking results with an
incorrect PDB file?

Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Dear sirs,
>
>
> After docking using autodock4, I saved the conformation of ligand in PDB
> file, but the  PDB file format had some problems, it's not correct. And when
> I used ligplot to detect the interaction between ligand and receptor, it
> could not detect the existence of the ligand because the problem of PDB
> format. So my question is how can I get the correct PDB format after docking
> using autodock4? Thanks very much!
>
>
> All the best!
>
> Qinghua
>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: about PDB file

Qinghua Liao
Hi Prof. Davide,

Thanks for your reply first. What I mean is that the PDB files I get are not standard format, so that they can't be detect by software ligplot, though it can be showed in Chimera. Here is an example that those line are parts of a pdb file got from docking using autodock4:

ATOM      1  N   <1> *          15.050  32.911  44.762  0.00  0.00      6p_2 N 
ATOM      2  C   <1> *          15.908  33.807  44.225  0.00  0.00      6p_2 C 
ATOM      3  C   <1> *          16.130  33.689  42.834  0.00  0.00      6p_2 C 
ATOM      4  C   <1> *          15.446  32.703  42.154  0.00  0.00      6p_2 C 
ATOM      5  N   <1> *          14.577  31.807  42.681  0.00  0.00      6p_2 N 
ATOM      6  C   <1> *          14.451  31.999  43.993  0.00  0.00      6p_2 C 
ATOM      7  S   <1> *          17.129  34.581  41.775  0.00  0.00      6p_2 S 
ATOM      8  C   <1> *          16.650  33.731  40.378  0.00  0.00      6p_2 C 
ATOM      9  N   <1> *          15.784  32.716  40.778  0.00  0.00      6p_2 N 

Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example. And also the name of the ligand, why does it appear the * character? Why are there two lines of 0.00? I can't understand that. Thanks very much!

All the best!

Qinghua



________________________________
From: Davide Mercadante <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 11:25:09 AM
Subject: Re: ADL: about PDB file

Hi Qinghua,

I don't understand sorry. How you can get the docking results with an
incorrect PDB file?

Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Dear sirs,
>
>
> After docking using autodock4, I saved the conformation of ligand in PDB
> file, but the  PDB file format had some problems, it's not correct. And when
> I used ligplot to detect the interaction between ligand and receptor, it
> could not detect the existence of the ligand because the problem of PDB
> format. So my question is how can I get the correct PDB format after docking
> using autodock4? Thanks very much!
>
>
> All the best!
>
> Qinghua
>
>
>
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



     
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Re: ADL: about PDB file

Davide Mercadante
Hi Qinghua,

sorry, I am not a professor but a modest PhD student...

However, you are alright that doesn't seem to be the proper pdb format
neither the pdbqt format. However, if you are able to open it with Chimera
have you tried to save it in a pdb format using chimera? Chimera should be
able to reproduce the original and common PDB format.

If Chimera doesn't work should work OpenBabel that is completely free and
sometimes useful...you will find it here:

http://en.wikipedia.org/wiki/OpenBabel

Hope this helps,
Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Hi Prof. Davide,
>
> Thanks for your reply first. What I mean is that the PDB files I get are
> not standard format, so that they can't be detect by software ligplot,
> though it can be showed in Chimera. Here is an example that those line are
> parts of a pdb file got from docking using autodock4:
>
> ATOM      1  N   <1> *          15.050  32.911  44.762  0.00  0.00
> 6p_2 N
> ATOM      2  C   <1> *          15.908  33.807  44.225  0.00  0.00
> 6p_2 C
> ATOM      3  C   <1> *          16.130  33.689  42.834  0.00  0.00
> 6p_2 C
> ATOM      4  C   <1> *          15.446  32.703  42.154  0.00  0.00
> 6p_2 C
> ATOM      5  N   <1> *          14.577  31.807  42.681  0.00  0.00
> 6p_2 N
> ATOM      6  C   <1> *          14.451  31.999  43.993  0.00  0.00
> 6p_2 C
> ATOM      7  S   <1> *          17.129  34.581  41.775  0.00  0.00
> 6p_2 S
> ATOM      8  C   <1> *          16.650  33.731  40.378  0.00  0.00
> 6p_2 C
> ATOM      9  N   <1> *          15.784  32.716  40.778  0.00  0.00
> 6p_2 N
>
> Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example.
> And also the name of the ligand, why does it appear the * character? Why are
> there two lines of 0.00? I can't understand that. Thanks very much!
>
> All the best!
>
> Qinghua
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 11:25:09 AM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> I don't understand sorry. How you can get the docking results with an
> incorrect PDB file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
> > Dear sirs,
> >
> >
> > After docking using autodock4, I saved the conformation of ligand in PDB
> > file, but the  PDB file format had some problems, it's not correct. And
> when
> > I used ligplot to detect the interaction between ligand and receptor, it
> > could not detect the existence of the ligand because the problem of PDB
> > format. So my question is how can I get the correct PDB format after
> docking
> > using autodock4? Thanks very much!
> >
> >
> > All the best!
> >
> > Qinghua
> >
> >
> >
> >
> > ________________________________________________
> > --- 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 ---
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Re: ADL: about PDB file

Qinghua Liao
Dear Davide,

Thanks for your suggestion first! And I have tried both of the two methods you mentioned, but it still doesn't work! Maybe it is a problem of autodock it self. Or you can have a try. Thanks once again!

Best wishes!

Sincere,

Qinghua Liao 




________________________________
From: Davide Mercadante <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 12:00:04 PM
Subject: Re: ADL: about PDB file

Hi Qinghua,

sorry, I am not a professor but a modest PhD student...

However, you are alright that doesn't seem to be the proper pdb format
neither the pdbqt format. However, if you are able to open it with Chimera
have you tried to save it in a pdb format using chimera? Chimera should be
able to reproduce the original and common PDB format.

If Chimera doesn't work should work OpenBabel that is completely free and
sometimes useful...you will find it here:

http://en.wikipedia.org/wiki/OpenBabel

Hope this helps,
Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Hi Prof. Davide,
>
> Thanks for your reply first. What I mean is that the PDB files I get are
> not standard format, so that they can't be detect by software ligplot,
> though it can be showed in Chimera. Here is an example that those line are
> parts of a pdb file got from docking using autodock4:
>
> ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
> 6p_2 N
> ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
> 6p_2 C
> ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
> 6p_2 C
> ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
> 6p_2 C
> ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
> 6p_2 N
> ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
> 6p_2 C
> ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
> 6p_2 S
> ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
> 6p_2 C
> ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
> 6p_2 N
>
> Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example.
> And also the name of the ligand, why does it appear the * character? Why are
> there two lines of 0.00? I can't understand that. Thanks very much!
>
> All the best!
>
> Qinghua
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 11:25:09 AM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> I don't understand sorry. How you can get the docking results with an
> incorrect PDB file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
> > Dear sirs,
> >
> >
> > After docking using autodock4, I saved the conformation of ligand in PDB
> > file, but the  PDB file format had some problems, it's not correct. And
> when
> > I used ligplot to detect the interaction between ligand and receptor, it
> > could not detect the existence of the ligand because the problem of PDB
> > format. So my question is how can I get the correct PDB format after
> docking
> > using autodock4? Thanks very much!
> >
> >
> > All the best!
> >
> > Qinghua
> >
> >
> >
> >
> > ________________________________________________
> > --- 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 ---



     
________________________________________________
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Re: ADL: about PDB file

Davide Mercadante
Did Chimera converted in the proper PDB format when you save the file?

Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Dear Davide,
>
> Thanks for your suggestion first! And I have tried both of the two methods
> you mentioned, but it still doesn't work! Maybe it is a problem of autodock
> it self. Or you can have a try. Thanks once again!
>
> Best wishes!
>
> Sincere,
>
> Qinghua Liao
>
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 12:00:04 PM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> sorry, I am not a professor but a modest PhD student...
>
> However, you are alright that doesn't seem to be the proper pdb format
> neither the pdbqt format. However, if you are able to open it with Chimera
> have you tried to save it in a pdb format using chimera? Chimera should be
> able to reproduce the original and common PDB format.
>
> If Chimera doesn't work should work OpenBabel that is completely free and
> sometimes useful...you will find it here:
>
> http://en.wikipedia.org/wiki/OpenBabel
>
> Hope this helps,
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
> > Hi Prof. Davide,
> >
> > Thanks for your reply first. What I mean is that the PDB files I get are
> > not standard format, so that they can't be detect by software ligplot,
> > though it can be showed in Chimera. Here is an example that those line
> are
> > parts of a pdb file got from docking using autodock4:
> >
> > ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
> > 6p_2 N
> > ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
> > 6p_2 C
> > ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
> > 6p_2 C
> > ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
> > 6p_2 C
> > ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
> > 6p_2 N
> > ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
> > 6p_2 C
> > ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
> > 6p_2 S
> > ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
> > 6p_2 C
> > ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
> > 6p_2 N
> >
> > Why the same atoms don't numbered as C1 C2 C3, taking carbon as an
> example.
> > And also the name of the ligand, why does it appear the * character? Why
> are
> > there two lines of 0.00? I can't understand that. Thanks very much!
> >
> > All the best!
> >
> > Qinghua
> >
> >
> >
> > ________________________________
> > From: Davide Mercadante <[hidden email]>
> > To: [hidden email]
> > Sent: Wednesday, July 29, 2009 11:25:09 AM
> > Subject: Re: ADL: about PDB file
> >
> > Hi Qinghua,
> >
> > I don't understand sorry. How you can get the docking results with an
> > incorrect PDB file?
> >
> > Cheers,
> > Davide
> >
> > 2009/7/29 Qinghua Liao <[hidden email]>
> >
> > > Dear sirs,
> > >
> > >
> > > After docking using autodock4, I saved the conformation of ligand in
> PDB
> > > file, but the  PDB file format had some problems, it's not correct. And
> > when
> > > I used ligplot to detect the interaction between ligand and receptor,
> it
> > > could not detect the existence of the ligand because the problem of PDB
> > > format. So my question is how can I get the correct PDB format after
> > docking
> > > using autodock4? Thanks very much!
> > >
> > >
> > > All the best!
> > >
> > > Qinghua
> > >
> > >
> > >
> > >
> > > ________________________________________________
> > > --- 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 ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: about PDB file

raghu bhagavat
In reply to this post by Qinghua Liao
I dont understand how you are getting the * mark in your file......Anyways the standard PDB format should be like this.....Go through this link
http://www.wwpdb.org/documentation/format32/sect9.html#MODEL

And dont worry about the 0.000 that are there in the 2 columns.....Ligplot will not recognize the complex if the atom names are not given and everything apart from this is correct......

Redock the same thing........if there is no residue name, then add for ex. UNK in the 18th-19th-20th column resp........remove off the <1> pattern......add say Residue number 501 in the columns 24-26 respectively....

Give a TER pattern before the ligand co-ords start......replace all the ATOM co-ords of the ligand to HETATM (again you have to be careful with the PDB standard format with respect to the columns)

Put an END pattern at the last....Then submit..........This should help........

Cheers,
Raghu Bhagavat

=======END OF STORY========

--- On Wed, 29/7/09, Qinghua Liao <[hidden email]> wrote:

From: Qinghua Liao <[hidden email]>
Subject: Re: ADL: about PDB file
To: [hidden email]
Date: Wednesday, 29 July, 2009, 10:15 AM

Dear Davide,

Thanks for your suggestion first! And I have tried both of the two methods you mentioned, but it still doesn't work! Maybe it is a problem of autodock it self. Or you can have a try. Thanks once again!

Best wishes!

Sincere,

Qinghua Liao




________________________________
From: Davide Mercadante <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 12:00:04 PM
Subject: Re: ADL: about PDB file

Hi Qinghua,

sorry, I am not a professor but a modest PhD student...

However, you are alright that doesn't seem to be the proper pdb format
neither the pdbqt format. However, if you are able to open it with Chimera
have you tried to save it in a pdb format using chimera? Chimera should be
able to reproduce the original and common PDB format.

If Chimera doesn't work should work OpenBabel that is completely free and
sometimes useful...you will find it here:

http://en.wikipedia.org/wiki/OpenBabel

Hope this helps,
Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Hi Prof. Davide,
>
> Thanks for your reply first. What I mean is that the PDB files I get are
> not standard format, so that they can't be detect by software ligplot,
> though it can be showed in Chimera. Here is an example that those line are
> parts of a pdb file got from docking using autodock4:
>
> ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
> 6p_2 N
> ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
> 6p_2 C
> ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
> 6p_2 C
> ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
> 6p_2 C
> ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
> 6p_2 N
> ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
> 6p_2 C
> ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
> 6p_2 S
> ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
> 6p_2 C
> ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
> 6p_2 N
>
> Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example.
> And also the name of the ligand, why does it appear the * character? Why are
> there two lines of 0.00? I can't understand that. Thanks very much!
>
> All the best!
>
> Qinghua
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 11:25:09 AM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> I don't understand sorry. How you can get the docking results with an
> incorrect PDB file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
> > Dear sirs,
> >
> >
> > After docking using autodock4, I saved the conformation of ligand in PDB
> > file, but the  PDB file format had some problems, it's not correct. And
> when
> > I used ligplot to detect the interaction between ligand and receptor, it
> > could not detect the existence of the ligand because the problem of PDB
> > format. So my question is how can I get the correct PDB format after
> docking
> > using autodock4? Thanks very much!
> >
> >
> > All the best!
> >
> > Qinghua
> >
> >
> >
> >
> > ________________________________________________
> > --- 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 ---



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Re: ADL: about PDB file

Qinghua Liao
In reply to this post by Davide Mercadante
No, the problems I told you in the last mail still exist after save file in PDB format using chimera. The same as openbabel.

All the best!

Qinghua Liao




________________________________
From: Davide Mercadante <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 1:14:46 PM
Subject: Re: ADL: about PDB file

Did Chimera converted in the proper PDB format when you save the file?

Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Dear Davide,
>
> Thanks for your suggestion first! And I have tried both of the two methods
> you mentioned, but it still doesn't work! Maybe it is a problem of autodock
> it self. Or you can have a try. Thanks once again!
>
> Best wishes!
>
> Sincere,
>
> Qinghua Liao
>
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 12:00:04 PM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> sorry, I am not a professor but a modest PhD student...
>
> However, you are alright that doesn't seem to be the proper pdb format
> neither the pdbqt format. However, if you are able to open it with Chimera
> have you tried to save it in a pdb format using chimera? Chimera should be
> able to reproduce the original and common PDB format.
>
> If Chimera doesn't work should work OpenBabel that is completely free and
> sometimes useful...you will find it here:
>
> http://en.wikipedia.org/wiki/OpenBabel
>
> Hope this helps,
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
> > Hi Prof. Davide,
> >
> > Thanks for your reply first. What I mean is that the PDB files I get are
> > not standard format, so that they can't be detect by software ligplot,
> > though it can be showed in Chimera. Here is an example that those line
> are
> > parts of a pdb file got from docking using autodock4:
> >
> > ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
> > 6p_2 N
> > ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
> > 6p_2 C
> > ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
> > 6p_2 C
> > ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
> > 6p_2 C
> > ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
> > 6p_2 N
> > ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
> > 6p_2 C
> > ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
> > 6p_2 S
> > ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
> > 6p_2 C
> > ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
> > 6p_2 N
> >
> > Why the same atoms don't numbered as C1 C2 C3, taking carbon as an
> example.
> > And also the name of the ligand, why does it appear the * character? Why
> are
> > there two lines of 0.00? I can't understand that. Thanks very much!
> >
> > All the best!
> >
> > Qinghua
> >
> >
> >
> > ________________________________
> > From: Davide Mercadante <[hidden email]>
> > To: [hidden email]
> > Sent: Wednesday, July 29, 2009 11:25:09 AM
> > Subject: Re: ADL: about PDB file
> >
> > Hi Qinghua,
> >
> > I don't understand sorry. How you can get the docking results with an
> > incorrect PDB file?
> >
> > Cheers,
> > Davide
> >
> > 2009/7/29 Qinghua Liao <[hidden email]>
> >
> > > Dear sirs,
> > >
> > >
> > > After docking using autodock4, I saved the conformation of ligand in
> PDB
> > > file, but the  PDB file format had some problems, it's not correct. And
> > when
> > > I used ligplot to detect the interaction between ligand and receptor,
> it
> > > could not detect the existence of the ligand because the problem of PDB
> > > format. So my question is how can I get the correct PDB format after
> > docking
> > > using autodock4? Thanks very much!
> > >
> > >
> > > All the best!
> > >
> > > Qinghua
> > >
> > >
> > >
> > >
> > > ________________________________________________
> > > --- 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 ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



     
________________________________________________
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Re: ADL: about PDB file

bagdevi
Check you original PDB of ligand you gave input for the autodock.
And after docking, how are you retrieving the pdb coordinates of the ligand?

Regards,
Bagdevi Mishra.




On Wed, Jul 29, 2009 at 10:52 AM, Qinghua Liao<[hidden email]> wrote:

> No, the problems I told you in the last mail still exist after save file in PDB format using chimera. The same as openbabel.
>
> All the best!
>
> Qinghua Liao
>
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 1:14:46 PM
> Subject: Re: ADL: about PDB file
>
> Did Chimera converted in the proper PDB format when you save the file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
>> Dear Davide,
>>
>> Thanks for your suggestion first! And I have tried both of the two methods
>> you mentioned, but it still doesn't work! Maybe it is a problem of autodock
>> it self. Or you can have a try. Thanks once again!
>>
>> Best wishes!
>>
>> Sincere,
>>
>> Qinghua Liao
>>
>>
>>
>>
>> ________________________________
>> From: Davide Mercadante <[hidden email]>
>> To: [hidden email]
>> Sent: Wednesday, July 29, 2009 12:00:04 PM
>> Subject: Re: ADL: about PDB file
>>
>> Hi Qinghua,
>>
>> sorry, I am not a professor but a modest PhD student...
>>
>> However, you are alright that doesn't seem to be the proper pdb format
>> neither the pdbqt format. However, if you are able to open it with Chimera
>> have you tried to save it in a pdb format using chimera? Chimera should be
>> able to reproduce the original and common PDB format.
>>
>> If Chimera doesn't work should work OpenBabel that is completely free and
>> sometimes useful...you will find it here:
>>
>> http://en.wikipedia.org/wiki/OpenBabel
>>
>> Hope this helps,
>> Cheers,
>> Davide
>>
>> 2009/7/29 Qinghua Liao <[hidden email]>
>>
>> > Hi Prof. Davide,
>> >
>> > Thanks for your reply first. What I mean is that the PDB files I get are
>> > not standard format, so that they can't be detect by software ligplot,
>> > though it can be showed in Chimera. Here is an example that those line
>> are
>> > parts of a pdb file got from docking using autodock4:
>> >
>> > ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
>> > 6p_2 N
>> > ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
>> > 6p_2 C
>> > ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
>> > 6p_2 C
>> > ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
>> > 6p_2 C
>> > ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
>> > 6p_2 N
>> > ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
>> > 6p_2 C
>> > ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
>> > 6p_2 S
>> > ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
>> > 6p_2 C
>> > ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
>> > 6p_2 N
>> >
>> > Why the same atoms don't numbered as C1 C2 C3, taking carbon as an
>> example.
>> > And also the name of the ligand, why does it appear the * character? Why
>> are
>> > there two lines of 0.00? I can't understand that. Thanks very much!
>> >
>> > All the best!
>> >
>> > Qinghua
>> >
>> >
>> >
>> > ________________________________
>> > From: Davide Mercadante <[hidden email]>
>> > To: [hidden email]
>> > Sent: Wednesday, July 29, 2009 11:25:09 AM
>> > Subject: Re: ADL: about PDB file
>> >
>> > Hi Qinghua,
>> >
>> > I don't understand sorry. How you can get the docking results with an
>> > incorrect PDB file?
>> >
>> > Cheers,
>> > Davide
>> >
>> > 2009/7/29 Qinghua Liao <[hidden email]>
>> >
>> > > Dear sirs,
>> > >
>> > >
>> > > After docking using autodock4, I saved the conformation of ligand in
>> PDB
>> > > file, but the  PDB file format had some problems, it's not correct. And
>> > when
>> > > I used ligplot to detect the interaction between ligand and receptor,
>> it
>> > > could not detect the existence of the ligand because the problem of PDB
>> > > format. So my question is how can I get the correct PDB format after
>> > docking
>> > > using autodock4? Thanks very much!
>> > >
>> > >
>> > > All the best!
>> > >
>> > > Qinghua
>> > >
>> > >
>> > >
>> > >
>> > > ________________________________________________
>> > > --- 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 ---
>>
> ________________________________________________
> --- 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 ---
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Re: ADL: about PDB file

Qinghua Liao
Dear Bagdevi Mishra,

Yes, you are right. It's the problem of the original PDB file format which I prepared using the general software. And now I find that pymol can solve this problem! Thanks for your reply!

All the best!

Qinghua Liao




________________________________
From: Bagdevi <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 1:56:49 PM
Subject: Re: ADL: about PDB file

Check you original PDB of ligand you gave input for the autodock.
And after docking, how are you retrieving the pdb coordinates of the ligand?

Regards,
Bagdevi Mishra.




On Wed, Jul 29, 2009 at 10:52 AM, Qinghua Liao<[hidden email]> wrote:

> No, the problems I told you in the last mail still exist after save file in PDB format using chimera. The same as openbabel.
>
> All the best!
>
> Qinghua Liao
>
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 1:14:46 PM
> Subject: Re: ADL: about PDB file
>
> Did Chimera converted in the proper PDB format when you save the file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
>> Dear Davide,
>>
>> Thanks for your suggestion first! And I have tried both of the two methods
>> you mentioned, but it still doesn't work! Maybe it is a problem of autodock
>> it self. Or you can have a try.. Thanks once again!
>>
>> Best wishes!
>>
>> Sincere,
>>
>> Qinghua Liao
>>
>>
>>
>>
>> ________________________________
>> From: Davide Mercadante <[hidden email]>
>> To: [hidden email]
>> Sent: Wednesday, July 29, 2009 12:00:04 PM
>> Subject: Re: ADL: about PDB file
>>
>> Hi Qinghua,
>>
>> sorry, I am not a professor but a modest PhD student...
>>
>> However, you are alright that doesn't seem to be the proper pdb format
>> neither the pdbqt format. However, if you are able to open it with Chimera
>> have you tried to save it in a pdb format using chimera? Chimera should be
>> able to reproduce the original and common PDB format.
>>
>> If Chimera doesn't work should work OpenBabel that is completely free and
>> sometimes useful...you will find it here:
>>
>> http://en.wikipedia.org/wiki/OpenBabel
>>
>> Hope this helps,
>> Cheers,
>> Davide
>>
>> 2009/7/29 Qinghua Liao <[hidden email]>
>>
>> > Hi Prof. Davide,
>> >
>> > Thanks for your reply first. What I mean is that the PDB files I get are
>> > not standard format, so that they can't be detect by software ligplot,
>> > though it can be showed in Chimera. Here is an example that those line
>> are
>> > parts of a pdb file got from docking using autodock4:
>> >
>> > ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
>> > 6p_2 N
>> > ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
>> > 6p_2 C
>> > ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
>> > 6p_2 C
>> > ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
>> > 6p_2 C
>> > ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
>> > 6p_2 N
>> > ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
>> > 6p_2 C
>> > ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
>> > 6p_2 S
>> > ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
>> > 6p_2 C
>> > ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
>> > 6p_2 N
>> >
>> > Why the same atoms don't numbered as C1 C2 C3, taking carbon as an
>> example.
>> > And also the name of the ligand, why does it appear the * character? Why
>> are
>> > there two lines of 0.00? I can't understand that. Thanks very much!
>> >
>> > All the best!
>> >
>> > Qinghua
>> >
>> >
>> >
>> > ________________________________
>> > From: Davide Mercadante <[hidden email]>
>> > To: [hidden email]
>> > Sent: Wednesday, July 29, 2009 11:25:09 AM
>> > Subject: Re: ADL: about PDB file
>> >
>> > Hi Qinghua,
>> >
>> > I don't understand sorry. How you can get the docking results with an
>> > incorrect PDB file?
>> >
>> > Cheers,
>> > Davide
>> >
>> > 2009/7/29 Qinghua Liao <[hidden email]>
>> >
>> > > Dear sirs,
>> > >
>> > >
>> > > After docking using autodock4, I saved the conformation of ligand in
>> PDB
>> > > file, but the  PDB file format had some problems, it's not correct. And
>> > when
>> > > I used ligplot to detect the interaction between ligand and receptor,
>> it
>> > > could not detect the existence of the ligand because the problem of PDB
>> > > format. So my question is how can I get the correct PDB format after
>> > docking
>> > > using autodock4? Thanks very much!
>> > >
>> > >
>> > > All the best!
>> > >
>> > > Qinghua
>> > >
>> > >
>> > >
>> > >
>> > > ________________________________________________
>> > > --- 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 ---
>>
> ________________________________________________
> --- 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 ---
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Re: ADL: about PDB file

Qinghua Liao
In reply to this post by raghu bhagavat
Dear Raghu Bhagavat,
 
Thanks for your reply and suggestion! And I have found the reason! Thanks!
 
All the best!
 
Qinghua Liao



________________________________
From: raghu bhagavat <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 1:19:43 PM
Subject: Re: ADL: about PDB file

I dont understand how you are getting the * mark in your file......Anyways the standard PDB format should be like this.....Go through this link
http://www.wwpdb.org/documentation/format32/sect9.html#MODEL

And dont worry about the 0.000 that are there in the 2 columns.....Ligplot will not recognize the complex if the atom names are not given and everything apart from this is correct......

Redock the same thing........if there is no residue name, then add for ex. UNK in the 18th-19th-20th column resp........remove off the <1> pattern......add say Residue number 501 in the columns 24-26 respectively....

Give a TER pattern before the ligand co-ords start......replace all the ATOM co-ords of the ligand to HETATM (again you have to be careful with the PDB standard format with respect to the columns)

Put an END pattern at the last....Then submit..........This should help........

Cheers,
Raghu Bhagavat

=======END OF STORY========

--- On Wed, 29/7/09, Qinghua Liao <[hidden email]> wrote:

From: Qinghua Liao <[hidden email]>
Subject: Re: ADL: about PDB file
To: [hidden email]
Date: Wednesday, 29 July, 2009, 10:15 AM

Dear Davide,

Thanks for your suggestion first! And I have tried both of the two methods you mentioned, but it still doesn't work! Maybe it is a problem of autodock it self. Or you can have a try. Thanks once again!

Best wishes!

Sincere,

Qinghua Liao




________________________________
From: Davide Mercadante <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 12:00:04 PM
Subject: Re: ADL: about PDB file

Hi Qinghua,

sorry, I am not a professor but a modest PhD student...

However, you are alright that doesn't seem to be the proper pdb format
neither the pdbqt format. However, if you are able to open it with Chimera
have you tried to save it in a pdb format using chimera? Chimera should be
able to reproduce the original and common PDB format.

If Chimera doesn't work should work OpenBabel that is completely free and
sometimes useful...you will find it here:

http://en.wikipedia.org/wiki/OpenBabel

Hope this helps,
Cheers,
Davide

2009/7/29 Qinghua Liao <[hidden email]>

> Hi Prof. Davide,
>
> Thanks for your reply first. What I mean is that the PDB files I get are
> not standard format, so that they can't be detect by software ligplot,
> though it can be showed in Chimera. Here is an example that those line are
> parts of a pdb file got from docking using autodock4:
>
> ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00
> 6p_2 N
> ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00
> 6p_2 C
> ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00
> 6p_2 C
> ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00
> 6p_2 C
> ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00
> 6p_2 N
> ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00
> 6p_2 C
> ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00
> 6p_2 S
> ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00
> 6p_2 C
> ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00
> 6p_2 N
>
> Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example.
> And also the name of the ligand, why does it appear the * character? Why are
> there two lines of 0.00? I can't understand that. Thanks very much!
>
> All the best!
>
> Qinghua
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 11:25:09 AM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> I don't understand sorry. How you can get the docking results with an
> incorrect PDB file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
> > Dear sirs,
> >
> >
> > After docking using autodock4, I saved the conformation of ligand in PDB
> > file, but the  PDB file format had some problems, it's not correct. And
> when
> > I used ligplot to detect the interaction between ligand and receptor, it
> > could not detect the existence of the ligand because the problem of PDB
> > format. So my question is how can I get the correct PDB format after
> docking
> > using autodock4? Thanks very much!
> >
> >
> > All the best!
> >
> > Qinghua
> >
> >
> >
> >
> > ________________________________________________
> > --- 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 ---



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Re: ADL: about PDB file

Nicolas Sapay
In reply to this post by Qinghua Liao
Hello,

That looks like a file created by Sybyl... Did you used Sybyl at some
point to prepare your protein?

Nicolas

Qinghua Liao a écrit :

> Hi Prof. Davide,
>
> Thanks for your reply first. What I mean is that the PDB files I get are not standard format, so that they can't be detect by software ligplot, though it can be showed in Chimera. Here is an example that those line are parts of a pdb file got from docking using autodock4:
>
> ATOM      1  N   <1> *          15.050  32.911  44.762  0.00  0.00      6p_2 N  
> ATOM      2  C   <1> *          15.908  33.807  44.225  0.00  0.00      6p_2 C  
> ATOM      3  C   <1> *          16.130  33.689  42.834  0.00  0.00      6p_2 C  
> ATOM      4  C   <1> *          15.446  32.703  42.154  0.00  0.00      6p_2 C  
> ATOM      5  N   <1> *          14.577  31.807  42.681  0.00  0.00      6p_2 N  
> ATOM      6  C   <1> *          14.451  31.999  43.993  0.00  0.00      6p_2 C  
> ATOM      7  S   <1> *          17.129  34.581  41.775  0.00  0.00      6p_2 S  
> ATOM      8  C   <1> *          16.650  33.731  40.378  0.00  0.00      6p_2 C  
> ATOM      9  N   <1> *          15.784  32.716  40.778  0.00  0.00      6p_2 N  
>
> Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example. And also the name of the ligand, why does it appear the * character? Why are there two lines of 0.00? I can't understand that. Thanks very much!
>
> All the best!
>
> Qinghua
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 11:25:09 AM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> I don't understand sorry. How you can get the docking results with an
> incorrect PDB file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>
>  
>> Dear sirs,
>>
>>
>> After docking using autodock4, I saved the conformation of ligand in PDB
>> file, but the  PDB file format had some problems, it's not correct. And when
>> I used ligplot to detect the interaction between ligand and receptor, it
>> could not detect the existence of the ligand because the problem of PDB
>> format. So my question is how can I get the correct PDB format after docking
>> using autodock4? Thanks very much!
>>
>>
>> All the best!
>>
>> Qinghua
>>
>>
>>
>>
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>>
>>    
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>
>
>      
> ________________________________________________
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>
>
>  

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Re: ADL: about PDB file

Qinghua Liao
Hi Nicolas,

Thanks for your reply! I use MOE to prepare the ligand, sometimes use chimera. Maybe that's the problem, because I find that the problem will disappear when I choose pymol to prepare the ligands. Thanks!

All the best,

Qinghua 




________________________________
From: Nicolas Sapay <[hidden email]>
To: [hidden email]
Sent: Wednesday, July 29, 2009 8:58:11 PM
Subject: Re: ADL: about PDB file

Hello,

That looks like a file created by Sybyl... Did you used Sybyl at some point to prepare your protein?

Nicolas

Qinghua Liao a écrit :

> Hi Prof. Davide,
>
> Thanks for your reply first. What I mean is that the PDB files I get are not standard format, so that they can't be detect by software ligplot, though it can be showed in Chimera. Here is an example that those line are parts of a pdb file got from docking using autodock4:
>
> ATOM      1  N  <1> *          15.050  32.911  44.762  0.00  0.00      6p_2 N  ATOM      2  C  <1> *          15.908  33.807  44.225  0.00  0.00      6p_2 C  ATOM      3  C  <1> *          16.130  33.689  42.834  0.00  0.00      6p_2 C  ATOM      4  C  <1> *          15.446  32.703  42.154  0.00  0.00      6p_2 C  ATOM      5  N  <1> *          14.577  31.807  42.681  0.00  0.00      6p_2 N  ATOM      6  C  <1> *          14.451  31.999  43.993  0.00  0.00      6p_2 C  ATOM      7  S  <1> *          17.129  34.581  41.775  0.00  0.00      6p_2 S  ATOM      8  C  <1> *          16.650  33.731  40.378  0.00  0.00      6p_2 C  ATOM      9  N  <1> *          15.784  32.716  40.778  0.00  0.00      6p_2 N 
> Why the same atoms don't numbered as C1 C2 C3, taking carbon as an example. And also the name of the ligand, why does it appear the * character? Why are there two lines of 0.00? I can't understand that. Thanks very much!
>
> All the best!
>
> Qinghua
>
>
>
> ________________________________
> From: Davide Mercadante <[hidden email]>
> To: [hidden email]
> Sent: Wednesday, July 29, 2009 11:25:09 AM
> Subject: Re: ADL: about PDB file
>
> Hi Qinghua,
>
> I don't understand sorry. How you can get the docking results with an
> incorrect PDB file?
>
> Cheers,
> Davide
>
> 2009/7/29 Qinghua Liao <[hidden email]>
>

>> Dear sirs,
>>
>>
>> After docking using autodock4, I saved the conformation of ligand in PDB
>> file, but the  PDB file format had some problems, it's not correct. And when
>> I used ligplot to detect the interaction between ligand and receptor, it
>> could not detect the existence of the ligand because the problem of PDB
>> format. So my question is how can I get the correct PDB format after docking
>> using autodock4? Thanks very much!
>>
>>
>> All the best!
>>
>> Qinghua
>>
>>
>>
>>
>> ________________________________________________
>> --- 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 ---
>
>


     
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