[gmx-users] question about aminoacids.rtp file when adding a new residue

Justin Lemkul jalemkul at vt.edu
Tue Sep 4 13:41:07 CEST 2012

On 9/4/12 7:37 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> I everybody,
> I add a phosphate to my structure. Now I want to minimize the structure.
> For this approach I have to add the serine with the phosphate as a new
> residue (SEP).
> To do this I first added it into the file "aminoacids.rtp". But here I
> have a question. Is the number after the atom the charge of the atom?

Yes.  There is a fully annotated .rtp entry in the manual, section 5.6.1.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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