[gmx-users] ligand

farial tavakoli farial.tavakoli at ymail.com
Sun Aug 13 19:14:07 CEST 2017

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear justin
Thank you for your replyI thought that topology file obtained from ATB needs to be changed like PRODRG

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On Sunday, August 13, 2017, 8:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 8/13/17 3:13 AM, ‪farial tavakoli‬ ‪ wrote:
> Dear GROMACS users
> I noticed my ligand has some broken bonds and changes in atoms arrengement after md simulation was done. I have read before that no bond is broken and created in simulation . So why have been ligand changed ?
> I think, i have to notice that when i wanted to create a ligand topology , i used ATB server to create topology and pdb files. and when wanted to reassign the charges and charge groups, noticed that some of the atoms of ligand that have to be in a charge group, were not successive  , so decided to rearrange them and replaced them to place them in a charge group.

Why did you modify the topology?  Usually ATB topologies require no 
modification.  If you "rearranged" atoms in any way, then you irreparably broke 
the topology because no all of the bonded interactions are nonsense.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129

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