Re: [AMBER] Selection of chain

From: David A Case <>
Date: Sat, 9 May 2015 22:37:29 -0400

On Sat, May 09, 2015, muhammad tahir ayub wrote:

> 1) my protein(4KIK) contain two protomers (a) and (b), both have the
> binding site, but protomer (b) undergo phosphorylation and make the SEP
> residue while the serine of protomer (a) does not undergo phosphorylation
> so which protomer should be used for molecular dynamics simulation.

I don't think people on the mailing list can answer this sort of question.
Only you know why you are doing this study, and what you hope to learn from

> 2) The histidine and cystein should be parameterized for the md simulation
> in Amber 12 OR NOT

It is hard to understand the question here: histidine and cysteine are among
the residues that are in standard libraries in all versions of Amber. (But I
am probably not understanding your question well.)


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Received on Sat May 09 2015 - 20:00:02 PDT
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