TBalius: Created page with " This page is written by Trent E. Balius (FNLCR) on March 28, 2020. This is for cases where the cofactor does not already have cofactors. For the receptor, I use Chimera'..."

2020-03-28T23:37:29Z

Created page with " This page is written by Trent E. Balius (FNLCR) on March 28, 2020. This is for cases where the cofactor does not already have cofactors. For the receptor, I use Chimera'..."

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This page is written by Trent E. Balius (FNLCR) on March 28, 2020.

This is for cases where the cofactor does not already have cofactors.

For the receptor, I use Chimera's DOCKprep module to remove solvent, add in missing atoms for residues, and remove alternative side-chains.

I run the blastermaster on the structure without the co factor to protonate the protein with reduce.

python $DOCKBASE/proteins/blastermaster/blastermaster.py --addhOptions=" -HIS -FLIPs " -v

I visualize the protonated receptor and make sure that it seems correct.

I prepare the co-factor in chimera adding the hydrogen to the structure. I then run antechamber on that protonated mol2 file using this csh script:

cat ../GTP_charge/002.cofprep.antechamber.csh
#! /bin/tcsh

# setenv AMBERHOME /nfs/soft/amber/amber14

set mountdir = `pwd`
set filedir = ${mountdir}/../

set workdir = ${mountdir}/cof

rm -rf $workdir; mkdir -p $workdir; cd $workdir

set charge = -4 # <--- you need to changes

cp $filedir/Q61L_GTP.pdb cof.pdb # <--- you need to changes
#cp $workdir/33443.pdb lig.pdb
#sed -i 's/<0> /LIG/g' lig1.mol2

$AMBERHOME/bin/antechamber -i cof.pdb -fi pdb -o cof.ante.mol2 -fo mol2
$AMBERHOME/bin/antechamber -i cof.ante.mol2 -fi mol2 -o cof.ante.charge.mol2 -fo mol2 -c bcc -at sybyl -nc ${charge}
$AMBERHOME/bin/antechamber -i cof.ante.mol2 -fi mol2 -o cof.ante.pdb -fo pdb
$AMBERHOME/bin/antechamber -i cof.ante.charge.mol2 -fi mol2 -o cof.ante.charge.prep -fo prepi
$AMBERHOME/bin/parmchk2 -i cof.ante.charge.prep -f prepi -o cof.ante.charge.frcmod

Add the co-factor to the dock parameter files.

Copy the default parameter files from DOCKBASE:
cp $DOCKBASE/proteins/defaults/prot.table.ambcrg.ambH $DOCKBASE/proteins/defaults/amb.crg.oxt .

Here are a python library and a python script that I use to to prepare the files to create amb.crg.oxt and prot.table.ambcrg.ambH for the cofactor
https://github.com/tbalius/teb_scripts_programs/blob/master/zzz.scripts/mol2.py
https://github.com/tbalius/teb_scripts_programs/blob/master/zzz.scripts/mol2toDOCK37type.py

Here is how to run the script:
python ${TEB_SCRIPTS_PATH}/zzz.scripts/mol2toDOCK37type.py ../GTP_charge/cof/cof.ante.charge.mol2 temp

Add the parameters generated from mol2toDOCK37type.py

cat temp.prot.table.ambcrg.ambH >> prot.table.ambcrg.ambH
cat temp.amb.crg.oxt >> amb.crg.oxt
Use a text editor like vim to check the file and remove white space.

rm working/ -rf; mkdir working; cp rec.crg.pdb working; $DOCKBASE/proteins/blastermaster/blastermaster.py --addNOhydrogensflag --chargeFile=`pwd`/amb.crg.oxt --vdwprottable=`pwd`/prot.table.ambcrg.ambH -v

Prepare a receptor with a cofactor for docking - Revision history

TBalius: Created page with " This page is written by Trent E. Balius (FNLCR) on March 28, 2020. This is for cases where the cofactor does not already have cofactors. For the receptor, I use Chimera'..."