Re: [AMBER] residue list

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 12 Aug 2011 20:30:09 -0400

There is a residue list in the topology file under RESIDUE_LABEL, or if you are talking about the ones used by leap, then they are in $AMBERHOME/dat/leap/lib/amino10.lib. The protonated form if ASP is ASH, protonated GLU is GLH, deprotonated LYS is LYN, and deprotonated CYS is CYM.

HTH,
Jason

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Aug 12, 2011, at 6:47 PM, "E. Nihal Korkmaz" <enihalkorkmaz.gmail.com> wrote:
> Dear all,
> 
> How can i find the residue list? I mean, different versions (according to
> protonation state) of Lys, Asp, Glu and Cys. I know the versions of His but
> i didn't come across anything for the other ionizable residues.
> 
> Best,
> 
> -- 
> Elif Nihal Korkmaz
> 
> Research Assistant
> University of Wisconsin - Biophysics
> Member of Qiang Cui & Thomas Record Labs
> 1101 University Ave, Rm. 8359
> Madison, WI 53706
> Phone:  608-265-3644
> Email:   korkmaz.wisc.edu
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Received on Fri Aug 12 2011 - 18:00:02 PDT