AMBER Archive (2001)

Subject: Re: residue numbering in dimers and trimers

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Aug 30 2001 - 12:00:44 CDT

        The numbering scheme in the PDB file is such that it is easy to
        indentify the monomers, but I know that tleap will number all the
        residues sequentially, which can be a bit of a pain when one when
        one wants to restrain the same residues in both monomers, and later
        when translating the *.xyz or *.crd files back into *.pdb ones. I
        wonder if there is any way to persuade tleap to preserve the original
        numbering scheme from the *.pdb file (or any numbering scheme which
        will allow easy identification of the monomers).
        
It would require some programming, adding the pdb info to the
redidue unit on input & using it for savepdb and saveamberparm.

If anyone wants to do it, I'll advise & incorporate the code
into the release.

Bill Ross