AMBER Archive (2009)

Subject: RE: [AMBER] lone pairs on CYX and MET

From: Ross Walker (
Date: Thu Jan 08 2009 - 12:17:52 CST

Hi John,

> 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>

It does not handle them. There effect is implicit in the parameterization so
you should just remove them from your pdb file. There are some extra point
force fields (designed mainly for use with polarization) that include extra
points explicitly (although not on Sulfur I believe). Either way in these
situations the extra points are treated as special cases and created as
needed by Leap they are not read from the pdb.
> Again, there is a FATAL message for all of the MET and CYX residues in
> the pdb file.

Just remove the lines with atom names LP1 and LP2 and reload into Leap and
you should be good to go.

> 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.

Which is what you appear to have done so you can just use the prmtop and
inpcrd files from this.

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
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