[gmx-users] addition of the .itp file of a new residue

Justin Lemkul jalemkul at vt.edu
Fri Nov 21 13:30:25 CET 2014

On 11/20/14 11:16 PM, soumadwip ghosh wrote:
> Thanks justin for your help. Just one question. The .itp file I made by
> using ParamChem and your university server, gave me the total charge for
> tetramethyl ammonium molecule + 1.1 (shown by qtot) while it should be 1
> actually. My system contained -22 negative charge and for my work I just
> need to neutralize the system. So, I added 20 tma via ci and nmol option.
> Now everything is going fine with the simulation but my question is can the
> +1.1 charge of discreet tma species hamper or overestimate the real
> dynamics and the interaction of DNA with the ions present.

A ligand charge of +1.1 is nonsensical.  Do not do simulations with such a 
broken topology.  I don't know how or why ParamChem would have generated such a 
topology; it checks for integer charge, so either something was wrong with your 
input or something was wrong with the way the conversion was done, but without 
the input and output files, there's no way to know.



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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