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
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Wed Aug 27 2014 - 03:30:02 PDT
