AMBER Archive (2002)

Subject: xleap

From: sara nunez (mbdtssn_at_hotmail.com)
Date: Fri Jan 04 2002 - 17:28:14 CST

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Dear Ambers

I am working with a biomolecule which has a non-standard residue, for which
I have had to develop some parameters. Up to here, there was no problem. I
saved the parm and coord files in xleap as well as the pdb.lib and
pdb.frcmod.
Then I performed some minimisations to this model, and a MD simulation. I am
willing to analyse further some specific snapshots of this MD. For this, I
used anal to extract the pdb's of these snapshots. But now I want to
edit/modify some parameters of these snapshots, and I must reload the pdb's
in xleap to do this.

My problem now is that when I load the old pdb.lib and pdb.frcmod along with
the new pdb files, the parameters which are still the same for the
non-standar residue, are not read in. And I am in the same situation as I
was before I developed all the parameters.

I thought that since only the coordinates have changed, loading the
pdb.lib/pdb.frcmod and then the pdb would be enough to read in all the
parameters.
Do I have to manually type in all the parameters. Does anyone know what I am
doing wrong?

Thank you, and any advice will be welcome.
sara nunez

Sara Nunez
Computational Chemistry Department
University of Manchester
sara.nunez_at_stud.man.ac.uk

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