[gmx-users] charge groups

Justin Lemkul jalemkul at vt.edu
Mon Jun 9 13:58:57 CEST 2014

Please keep the discussion on the mailing list.

On 6/9/14, 3:02 AM, Negar Parvizi wrote:
> Dear Dr.Lemkul,
> Thank you very much for your reply. It was very helpful to me.
> I checked the force field .rtp files. Here I have two questions:
> 1-Checking the .rtp files of gromos force field, I saw that always  one hydrogen
> of NH2 and also the OH group of COOH were not included in the charge groups.

Only in the case of peptide bonds.  Free amines and acids are absolutely present 
in the force field.  Each constitute a single charge group.

> On the other hand, in your paper ( Practice Consideration for building
> GROMOS-Compatiple Small-Molecule Topologies) I noticed that you have replaced
> these NH2 and COOH groups with NHCH3 and COCH3. I did not understand this. Would
> you please explain why you did that ?

Each constitutes three atoms (CH3 is united), so it's physically very small. 
The point of charge groups (which is quickly becoming outdated, if not already 
so) is that neighbor searching is done based on some small unit of neutral or 
integer charge.

> Should we do the same modifications  for all NH2 and COOH groups, either when
> these groups belong to an aminoacid or any other molecule?

Absolutely not.  You shouldn't modify the chemistry of the molecule unless 
there's a functional purpose.  We capped the amino acids in that study because 
we wanted to study the dynamics of dipeptides, not zwitterionic forms in which 
charge effects may have unnecessarily dominated.

> 2- Is there any straightforward strategy for specifying charge groups of
> a ligand? If so, could you please introduce me a reference for that?

See above, and the discussion in the manual.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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