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

[Justin Lemkul]

On 9/4/12 7:51 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> 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?

Unless someone has already published suitable parameters (and many force fields 
can deal with phosphorylated residues), you have to derive them yourself.

http://www.gromacs.org/Documentation/How-tos/Parameterization

-Justin

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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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