[gmx-users] Calculating atom charges for ester

Justin Lemkul jalemkul at vt.edu
Fri Dec 13 14:02:40 CET 2013

On Fri, Dec 13, 2013 at 6:38 AM, pp0ta187 <p0ta at live.com> wrote:

> Dear forum users,
> I am new to MD and looking for help and a little tutorial how to create a
> .gro/.pdb file and calculate atom charges for a molecule I can not find
> online. I have assembled the molecule's .itp file and I seek help how to
> calculate charges with OPLS.
> molecule: 4-Methoxyphenyl dichloroacetate
Coordinate files can be constructed with any number of programs, some of
which are listed at
 For charges, the Kaminski et al. 2001 paper (the full reference is in the
Gromacs manual) has the full parametrization procedure in excellent detail,
including the exact method for calculating charges and how one goes about




Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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