The Molecular Graphics Laboratory Forum

AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
It is currently Sun Oct 26, 2014 4:19 am

All times are UTC




Post new topic Reply to topic  [ 5 posts ] 
Author Message
PostPosted: Sun Apr 08, 2012 10:48 pm 
Offline
Micromolar User
Micromolar User
User avatar

Joined: Fri Sep 30, 2011 12:36 pm
Posts: 11
First, thanks for letting the people freely use this software. Im trying to make some dockings using a chelating agent on a determined protein. The thing is I want to do the docking not only with the chelating agent itself, but also with some chelating agent-ion complexes. The question is how to do a pdbqt file that recognises that the ion and the chelating agent are not bonded, or this doesn't actually matter for Vina? Hope someone could answer me. Thanks in advance.
S. Schott.


Top
 Profile  
 
PostPosted: Tue Apr 10, 2012 9:32 pm 
Offline
MGL member
MGL member
User avatar

Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
SSchott wrote:
First, thanks for letting the people freely use this software. Im trying to make some dockings using a chelating agent on a determined protein. The thing is I want to do the docking not only with the chelating agent itself, but also with some chelating agent-ion complexes. The question is how to do a pdbqt file that recognises that the ion and the chelating agent are not bonded, or this doesn't actually matter for Vina? Hope someone could answer me. Thanks in advance.
S. Schott.


The geometric constraints are already embedded in PDBQT (which atoms can move relative to each other). These obviously matter in docking. Vina infers the bonding info from PDBQT based on the geometric constraints, and the distances. The bonds are used to type some atoms (e.g. which carbons are hydrophobic). However which atoms are H-donors or H-acceptors is already stated by the PDBQT. The interaction of a metal and other atoms is not affected by the covalent bonds the metal forms, I believe, except 1-4 interactions, which are always excluded.

_________________
If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.


Top
 Profile  
 
PostPosted: Tue Apr 10, 2012 9:40 pm 
Offline
Micromolar User
Micromolar User
User avatar

Joined: Fri Sep 30, 2011 12:36 pm
Posts: 11
Thank you for the answer. I certainly understand the flexibility constraints in the pdbqt (which I made thinking of the complex as a rigid molecule). I'm understanding that this "bonds" don't actually matter (I'm right?), but the thing is if what I'm seeing with ADT is what Vina interprets too, and if that "bonds" (generated between the metal and the chelating agent in ADT, but not in other viewers like PyMol) matter for the docking itself.


Top
 Profile  
 
PostPosted: Tue Apr 10, 2012 10:24 pm 
Offline
MGL member
MGL member
User avatar

Joined: Mon Oct 20, 2008 9:39 pm
Posts: 202
SSchott wrote:
Thank you for the answer. I certainly understand the flexibility constraints in the pdbqt (which I made thinking of the complex as a rigid molecule). I'm understanding that this "bonds" don't actually matter (I'm right?), but the thing is if what I'm seeing with ADT is what Vina interprets too, and if that "bonds" (generated between the metal and the chelating agent in ADT, but not in other viewers like PyMol) matter for the docking itself.


Vina only sees what's in the PDBQT, and PDBQT does not contain explicit info about the covalent bonds. These need to be inferred by Vina. The inferred bonds may be important in docking, as my previous message was trying to detail. However, the procedures used for inferring the bonds in Vina are unrelated to those used in PMV.

_________________
If you don't get your question answered here, consider posting it on the AutoDock mailing list instead of this forum. Please do not email or PM me with requests for help.


Top
 Profile  
 
PostPosted: Tue Apr 10, 2012 10:36 pm 
Offline
Micromolar User
Micromolar User
User avatar

Joined: Fri Sep 30, 2011 12:36 pm
Posts: 11
Thank you very much for your quick answer and for the software Dr. Trott. I'll continue doing the docking more relieved, expecting that what I'm doing is not complete nonsense.


Top
 Profile  
 
Display posts from previous:  Sort by  
Post new topic Reply to topic  [ 5 posts ] 

All times are UTC


Who is online

Users browsing this forum: No registered users and 1 guest


You cannot post new topics in this forum
You cannot reply to topics in this forum
You cannot edit your posts in this forum
You cannot delete your posts in this forum
You cannot post attachments in this forum

Search for:
Jump to:  
POWERED_BY
Translated by MaĆ«l Soucaze © 2009 phpBB.fr