[gmx-users] on the gmx solvate command

[Justin Lemkul]

On 6/4/15 4:09 AM, Brett wrote:
> Dear All,
>
>
> Before I neutralize my system with the genion command, I solvate it  with the gmx solvate command, it writes, "System total charge: 0.00". But the pdb2gmx step clearly indicate the systemp has -62 negative charges.
>
>
> Will you please explain to me why the gmx solvate step can show the system as without charge?
>

Because solvate reads in coordinates (which have no topological information). 
It uses the topology only to update it with the number of water molecules it 
adds, nothing else.  Tools that are knowledgeable about the topology (pdb2gmx, 
genion, grompp) can determine and correctly report the net charge.  Technically 
solvate can read in a .tpr, in which case it would know the correct charge. 
That output should probably just be disabled in the case of a plain coordinate 
file, but it's a minor thing.

-Justin

-- 
==================================================

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

==================================================