[gmx-users] core dumped

Justin Lemkul jalemkul at vt.edu
Sun Dec 28 21:03:46 CET 2014

On 12/27/14 4:22 PM, elham tazikeh wrote:
> Dear Justin
> thanks for your advise
> only my remained question is, if my problem was for my topology file (as i
> recieved this error a few times: your topology file has non-zero charge =
>   -0.619999)
> by editing my topology file (.itp file), can i going on my simulation?

Whatever editing you did was wrong if you end up with such a horrendous 
fractional charge.

> please tell me, what is the best way for distribute the charges on a
> molecule (Aspirin)?

All of the necessary functional groups are available in the Gromos force field 
(presumably that's what you're after since you were using PRODRG); the aromatic 
ring and carboxylic acid are standard components of the protein force field and 
the methyl ester group has had its parameters published recently.  For Gromos 
force fields, the transferability is very good, you usually just need to piece 
together existing groups.  For a drug molecule, a partition coefficient is 
likely readily available and serves as an excellent experimental target datum 
for verifying that your topology is reasonable.



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


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