It is possible that the atom names in the PDB are slightly different
than the atom names in the parameter files you are using. If this is
the case you can try deleting the OG1 atom of TPO in your PDB (make a
backup first!) and loading the modified PDB into leap to see if leap
places the atom in for you. You should get a message like 'Added X
missing heavy atoms'. If you don't get any errors make sure you still
visually inspect the resulting structure to make sure everything is
where it should be.
-Dan
On Tue, Sep 28, 2010 at 9:36 AM, fancy2012 <fancy2012.yeah.net> wrote:
> 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 - 09:00:10 PDT
