[gmx-users] Charge of the system

[Emran Heshmati]

 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
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