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

reisingere at rostlab.informatik.tu-muenchen.de reisingere at rostlab.informatik.tu-muenchen.de
Tue Sep 4 13:51:06 CEST 2012

Ah okey, thank you.
But now I have another question. Where can I get the charge and the
chargegroup of the atoms of my residue?
I have a serine with a phosphate on it. But I do not know the charges of
the atoms. Can you give me a hint where I can find them?
Thank you
> 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
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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