[gmx-users] About charge group

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 25 03:37:54 CEST 2009

wuxiao wrote:
> Dear gmx users, Recently, some questions puzzle me too much. While reading
> many resources, I can not think out. Therefore, I would like to turn for this
>  mail-list. These questions are as follows: (1) The total number of partial
> atom charge by summing the residue must be zero?

No, it must sum to the net charge on the residue.  For example, aspartate at pH
7 has a net -1 charge, so it will not sum to zero.

> (2) It can set several atoms into a charge group, which is neighbour covalent
> but on different residues?

I'm not quite clear on what you mean, but you can bridge two residues with
independent charge groups.  See, for example, the monosaccharides in the
Gromos96 .rtp files; hemiacetal linkages can span two different residues.

> (3) There are some tools, which can help set the number of charge group
> (cgnr)?

Typically, assign them by analogy to similar functional groups that already exist.


> Any reply would be thanked very much.
> Sincerely Chaofu Wu
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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