Hi,
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
quit
EOF
Scott
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Received on Sun Jun 24 2007 - 06:07:18 PDT
