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 - 01:00:04 PDT
