Hi Chris,
yes, I think this might be useful for me. Previously I've used pdb2pqr
server to proceed my pdb and obtain amber-like pdbs but it is not very
comfortable to work in case of the ensembles of pdb.
Kind regards,
James
2014-08-27 13:33 GMT+04:00 Chris Gao <yuhuigao.mail.dlut.edu.cn>:
> http://biophysics.cs.vt.edu/index.php
>
> Is this you need?
>
>
> > -----原始邮件-----
> > 发件人: "James Starlight" <jmsstarlight.gmail.com>
> > 发送时间: 2014年8月27日 星期三
> > 收件人: "AMBER Mailing List" <amber.ambermd.org>
> > 抄送:
> > 主题: [AMBER] Prediction of the protonation state for the ensemble of pdb
> structures
> >
> > Dear Amber users!
> >
> > I'm looking for the software for the prediction of the protonation states
> > of the titrable (asp, glu, his) residues for the ensemble (not single) of
> > the pdb structures. E.g I've made 100 models of my protein by modeller
> > which are differs in the conformation of the flexible loop where there
> were
> > alot of His, Asp and Glu residues. Depending on the conformation of the
> > loop this residues can be buried or exposed to solvent so it's
> protonation
> > states is differ. I'd like to obtain some statistics of the possible
> > protonation states for the given set of the structures differs in the
> > conformation of this flexible loop.
> >
> > I'll be very thankful for any suggestions.
> >
> >
> > James
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Received on Wed Aug 27 2014 - 03:00:02 PDT
