Hi. James!
It seems that yours residue cannot be recognised by programe. You may have a look at the 'FAQ' of H++ website, you can see 'Q:How can I cap protein termini? ' section.
I think this may help you.
Best,
Chris
> -----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: Re: [AMBER] Prediction of the protonation state for the ensemble of pdb structures
>
> could you also suggest me what should be done with the error
>
> FAILURE: Sequence discontinuity occurred between residues 289 and 1 at the
> line ATOM 1 N ASP 1 62.482 8.961 22.846 1.00103.76 N
>
> here I provide multi state (NNR format) of my conformers in single pdb
> which has 1 residue at the beginning and 289 at the end so no any
> connections between both should be included.
>
> James
>
>
> 2014-08-27 11:39 GMT+02:00 James Starlight <jmsstarlight.gmail.com>:
>
> > 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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> >>
> >
> >
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Received on Wed Aug 27 2014 - 05:30:02 PDT
