AMBER Archive (2009)

Subject: Re: [AMBER] database

From: case (
Date: Wed Sep 16 2009 - 11:53:56 CDT

On Wed, Sep 16, 2009, Steve Seibold wrote:
> Thanks Prof. Case for your response.
> Here is what I have written in my
> Source leaprc.ff03
> Source leaprc.gaff
> Loadamberparams ligand.frcmod
> Loadmol2 ligand.mol2

This won't work: you need to say "RES = loadMol2 ligand.mol2". Otherwise
the name of the residue won't get properly loaded into LEaP. Here "RES"
should be whatever the name of your residue is (DCP I guess).

However, the pdb file you supply is very weird: you have a bunch of TER
cards in the middle of residue 201. Those should not be there in the
input ligand.pdb. If Amber is adding them, something is wrong. But first,
fix the syntax of the loadMol2 command, and let's work from there.


AMBER mailing list