Dear fancy,
>> 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?
is this the only error?
Please ensure, that the residue name in your pdb file ("TPO") matches
the residue name of the phosphorylated amino acid in the parameter file.
As far as I can see, no residue from the Bryce site has the name TPO.
If it's only one single atom, you can follow Daniel's suggestion: Simply
delete the offending atom and have leap re-build it for you. But check
the resulting structures carefully.
In case you are not sure which atom has which name from the parameter
file, you can easily create a simple pdb file with leap using the
"sequence" command e.g.
# pdb file of serine phosphate
source leaprc.ff99SB
source leaprc.gaff
loadoff S2P.off
a=loadamberparams frcmod_s2p
s=sequence {ACE S2P NME}
savepdb s ace-s2p-nme.pdb
quit
Or you may display the parameterized residue within xleap.
However, you have to make sure, that all atoms and residue names from
your pdb file do match those from the parameter file.
Regards,
Anselm
Bioinformatik
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
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Received on Wed Sep 29 2010 - 01:30:03 PDT
