Re: AMBER: 5 Ligands and 1 Protein

From: Scott Brozell <>
Date: Wed, 20 Jun 2007 17:25:05 -0700


On Wed, 20 Jun 2007, Colby C wrote:

> I am trying to prepare files for SANDER to run energy minimization of a
> large protein with 5 ligands in 5 separate binding sites. We ran
> antechamber with each of the 5 ligands and it made the 5 prepin files.
> These files don't seem to have any missing parameters after running
> parmchck. We are not sure how to combine these ligands with the large
> protein. In xleap we tried to input each ligand but the xyz was all
> wrong. Ultimately we just want to put all 5 ligands in the protein and
> minimize the whole system.

Why were the Cartesian coordinates wrong ?

In UCSF DOCK we use LEaP to build a complex from a single receptor and
a single ligand. This would seem to be viable for five ligands.
After the receptor and ligand have been processed we combine them
with this LEaP command sequence:

cat << EOF > $leapin
 logFile $leap_log
 # LEaP called by $0
 source leaprc.ff94
 source leaprc.gaff
 source leaprc.dock.ions
 source leaprc.dock.cofactors
 # Begin DOCK Amber Score complex specific processing
 frcmod=loadamberparams $ligand_name.frcmod
 $ligand_name=loadMol2 $ligand_name.gaff.mol2
 x=loadPdb $receptor_name.amber.pdb
 z=combine { x $ligand_name }
 savePdb z $output_pdb
 saveAmberParm z $output_prmtop $output_inpcrd


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Received on Sun Jun 24 2007 - 06:07:18 PDT
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