I would like to know how Amber handles lone pairs of electrons on sulfur
atoms. I am trying to load the pdb file of a protein into xleap. I get
error messages like the following:
Created a new atom named: LP1 within residue: .R<MET 322>
Created a new atom named: LP2 within residue: .R<MET 322>
I get these messages for all of the methionine and cysteine residues in
the pdb file of the protein. When I try to do "saveAmberParm" I get the
following messages:
FATAL: Atom .R<MET 322> .A<LP1 18> does not have a type.
FATAL: Atom .R<MET 322> .A<LP2 19> does not have a type.
Again, there is a FATAL message for all of the MET and CYX residues in
the pdb file.
And the parameter file is not saved.
I can get the file to save if I go into the pdb file and delete all of
the lines referring to LP's. I don't like to do this because I think
that I am leaving out some critical information.
Can someone tell me how I can remedy the problem?
Thanks!
John Beale
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Received on Fri Jan 09 2009 - 01:21:53 PST
