[gmx-users] Re: non-neutralized system

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 12 13:46:51 CEST 2011

I have asked you before to keep all discussion on the gmx-users list.  Please do 
so.  It exists so that users can ask these types of questions and that others in 
the community can learn and contribute.

I don't understand why you're running pdb2gmx on a system that already has a 
topology and is fully constructed.  You only ever need to run pdb2gmx once to 
build the initial topology.  What's more, its output is not necessarily 
reflective of the entire system.  It prints charges on a per-molecule basis. 
Your protein will of course always have a +1 charge, so pdb2gmx tells you that. 
  I do not know if it will print the charges of ions that it finds, although the 
intended purpose of pdb2gmx is not for complex systems like this, so it may not 
print that information at all.

The only tool designed to expand the entire system topology into a complete 
description is grompp.  As long as it says the net charge is what you think it 
should be (in this case, zero), there is no problem.  Charges cannot change over 
time; they are fixed.


Zahra Kayani wrote:
> Dear, Dr. Lemkul
> I so sorry for asking my question directly with mailing, but I search a 
> lot and did not find my answer, my question is:
> I work on a protein with 528 residue and total charge of (-1) in top 
> files, so in  genion for neutralizing my system I add one NA+, but when 
> I check total charge of system in npt and md steps from their .*gro* 
> file with pdb2gmx command (pdb2gmx -f npt.gro -o output.gro -ignh -p 
> output.top -water spce) it was +1 and it mean that my system was not 
> neutralized, so I want ask you, what may be happen? and what should I do 
> for solving this problem?
> If you help me for solving my problem I never forget your help.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list