AMBER Archive (2009)

Subject: [AMBER] lone pairs on CYX and MET

From: Beale, John (jbeale_at_stlcop.edu)
Date: Thu Jan 08 2009 - 12:08:42 CST

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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