Dear Anselm,
Thanks very much for your explanations! I have realize what my problems is. Thank you again!
All the best,
fancy
At 2010-09-28，"Anselm Horn" <Anselm.Horn.biochem.uni-erlangen.de> wrote:
>Dear fancy,
>
>> In my complex, there are some nonstandard residues, SEP and TPO,
>> so I download these parameters from this website
>> http://www.pharmacy.manchester.ac.uk/bryce/amber/ ,
>> but I find that they can't match SEP and TPO.
>> I don't know what this problem is?
>> Could someone explain it for me, or give me some suggestion?
>
>most probably, the atom names for the phosphorylated amino acids in your
>pdb file do not match those of the downloaded parameter file.
>
>Look into the provided OFF files, where you find the atom names of the
>parameterized amino acids in the first table (e.g. for T2P OFF file
>"!entry.T2P.unit.atoms table") and change the atom names in your pdb
>file accordingly.
>
>Also make sure, that you use the correct residue name; in case you
>decide to apply the parameters from the Sticht group, the residues are
>named according to their charge state: S1P=singly charged serine
>phosphate, Ser-PO3H(1-); S2P=doubly charged serine phosphate, Ser-PO3(2-).
>
>Regards,
>
>Anselm
>
>Bioinformatik
>Friedrich-Alexander-Universität Erlangen-Nürnberg
>Germany
>
>
>
>
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Received on Tue Sep 28 2010 - 02:00:03 PDT
