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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.