[gmx-users] Charge of the system

Emran Heshmati heshmaty at yahoo.com
Tue Apr 28 17:15:00 CEST 2015

 Dear allI am using gromacsto simulate ligand bonding to an enzyme. I have two problems withcharge of system: 1) after making topology file for ligand using prodrug, I saw itsnet charge was -0.4. how can I neutralize it?2) I used this topology parameters of ligand to continuesimulation steps. After adding these parameters to protein topologyfile (as proposed by Lemkul) , the net charge of the system waschanged from 0 to -4. Is it needed to neutralize the system again oranything els?   
 Best Regards
Emran Heshmati Ph. D.Biophysicist,Computational  Bio-Chemist
P Save a tree... please don't print this e-mail unless you really need to

More information about the gromacs.org_gmx-users mailing list