[gmx-users] ligand

‪farial tavakoli‬ ‪ farial.tavakoli at ymail.com
Sun Aug 13 09:13:28 CEST 2017

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. 
I dont know if it is possible the brocken bonds in the ligand after simulation for 1 ns because of its topology?I am using gromacs 2016.3 and gromos96 54 a7 ff.

thanks in advanceTavakoli

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