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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Received on Wed Nov 18 2009 - 00:00:02 PST
