Dear Anselm,
Thanks very much for your explanations for my problem! Parts of the problems have been solvated following as you mentioned in last mail. But leap still shows the error like this: FATAL: Atom .R<TPO 197>.A<OG1 19> does not have a type. I can't explain why only OG1 of TPO doesn't have a type while others have? Could you do me a favor again? Thanks very much!
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 - 07:00:04 PDT
