[gmx-users] Ligand topology

farial tavakoli farial.tavakoli at ymail.com
Mon Jul 24 21:04:03 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 gromacs users
Is there any way to create ligand topology file by using pdb2gmx instead of prodrg? Because i use gromos 43a1 ff for making protein topology and use prodrg to create ligand topoligy and .gro file. But i dont know anything about reparametrizing the ligand topology but reassigning charge and charge groups. Is there anyone can help me:1) is it possible to make ligand topology file by pdb2gmx 2) what kind of reparametrizations are needed to be done to obtain the proper ligand topol.top file but reassigning charges and charge groups that 

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