AMBER Archive (2009)

Subject: Re: [AMBER] combining parameter files of ligand and enzyme

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Nov 18 2009 - 01:49:23 CST

Dear Ben,

> I am trying to combine parameters and coordinates of a ligand and an enzyme
> into one single file for use in MD simulations in Amber. I was wondering
> what was the best way, using tleap, to combine the two into one
> coordinate/parameter file.

- You need to have a PDB file of your complex.
- Then, the atom names & residue names in this PDB file have to match
these in the force field topology database you are going to load in
LEaP.
See http://archive.ambermd.org/200910/0191.html for instance for more
information

- You could follow this plan in LEaP:

# load the force field & force field topology database you need
source leaprc.xxxx
# load the force field library corresponding to your ligand
# (just use the mol2 file format)
LIG = loadmol2 yourlig.mol2
# load the PDB file of your complex
CMX = loadpdb complex.pdb
=> the recognition between the set of FF libraries & the PDB file
occurs only if the atom names & residue names in this PDB file match
these in the force field topology database & ligand FF library.

regards, Francois

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