[gmx-users] ligand

[Justin Lemkul]

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

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

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