[gmx-users] Charge of the system

[Justin Lemkul]

On 4/28/15 11:14 AM, Emran Heshmati wrote:
> 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

If the net charge on the ligand is -0.4, your topology is wrong.  PRODRG 
shouldn't have given that output, so if you're messing with the charges, you've 
made a mistake.  You'll have to fix the charges properly from PRODRG; they're 
generally wrong.

> 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?

Solve the above issue before doing anything else.  The observation of adding a 
ligand and changing the net charge of the system by -4 is inconsistent with the 
above description of your ligand topology.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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