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
Sent from Yahoo Mail for iPhone
On Sunday, August 13, 2017, 8:43 PM, Justin Lemkul <jalem...@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
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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry
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jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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