[gmx-users] Calculating atom charges for ester

[Justin Lemkul]

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
http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources.
 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
validation.

-Justin

-- 

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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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