Tutorial on running Molecular Dynamics for GIST grid generation

Tutorial written by Trent Balius (Jan. 9, 2017).

Here are more GIST related tutorials: DOCK_3.7_with_GIST_tutorials

Disclaimer

This is foremost for training Shoichet lab members. But we hope that the community finds this useful.

To use this tutorial you will need the following:

• AMBER12 or higher. Here I used AMBER14.
• AMBERTOOLS.
• GPUs to run AMBER on. In our case we uses an SGE queuing system to manage these jobs.
• It is helpful if you have DOCK3.7 the latest version.

Introduction

Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodynamic properties of water on GIST lattice.

Here, we will use these grids for DOCKing (although, there are many other uses).

Set up environment

you can add the following to your environment file (.cshrc) for just issue them on the command line.

source python with bio_python package.

source /nfs/soft/python/envs/complete/latest/env.csh

set DOCKBASE

setenv DOCKBASE "/nfs/home/tbalius/zzz.github/DOCK"

set AMBERHOME

 setenv AMBERHOME /nfs/soft/amber/amber14

Put msms in your path

set path = ( /nfs/home/tbalius/zzz.programs/msms $path )

Set up directories

cd /nfs/work/yourusername/

mkdir ambergisttutorial
cd ambergisttutorial 

Prepare for AMBER

• download 4NVE form the PDB brake it into receptor and ligand pieces.

• download pdb 4NVA form the PDB align it to 4NVE and out put waters that are close to the ligand.

• here is one way to do it:

(0) copy a file that msms needs:

 ln -s /nfs/home/tbalius/zzz.programs/msms/atmtypenumbers .

(1) Break up the protein from the ligand. run be_blasti.py

 mkdir 4NVE
 cd 4NVE
 python $DOCKBASE/proteins/pdb_breaker/be_blasti.py --pdbcode 4NVE nocarbohydrate original_numbers | tee -a pdbinfo_using_biopython.log
 cd ../
 mkdir 4NVA
 cd 4NVA
 python $DOCKBASE/proteins/pdb_breaker/be_blasti.py --pdbcode 4NVA nocarbohydrate original_numbers | tee -a pdbinfo_using_biopython.log
 cd ../

 cd 4NVE 
 sed -e "s/HETATM/ATOM  /g" lig.pdb > xtal-lig.pdb
 cd ../

 cd 4NVA
 grep HOH $mountdir/workingdir/4NVA/4NVA_A.pdb > $workdir/water.pdb
 cd ../

(2) Next align the two receptors (4NVE to 4NVA) and find those waters close to the ligand.

 mkdir aligned
 cd aligned

create file named "chimera.com" and write the following into the file:

 # Gist template #0
 open ../4NVA/rec.pdb
 # 4NVE rec
 open ../4NVE/rec.pdb
 # 4NVE lig
 open ../4NVE/lig.pdb
 # 4NVA waters
 open ../4NVA/water.pdb
 mmaker #0 #1
 matrixcopy #1 #2
 sel #3:HOH & #2 z<8
 del #3 & ~sel
 write format pdb  0 template.pdb
 write format pdb  1 aligned.rec.pdb
 write format pdb  2 aligned.lig.pdb
 write format pdb  3 close.waters.pdb

 /nfs/soft/chimera/current/bin/chimera --nogui chimera.com > & chimera.com.out

 cd ../

(3) Now lets run tleap.

(3.1) run leap to renumber residues.

mkdir tleap
cd tleap
cp ../aligned/template.pdb rec.pdb
cp ../aligned/close.waters.pdb wat.pdb

produces tleap input file named tleap.rec.1.in

set default PBradii mbondi2
# load the protein force field
source leaprc.ff14SB
loadamberparams frcmod_teb_mf_mod.hemall
loadamberprep heme_all_plus1.in
REC = loadpdb rec.pdb
# draw bond between HIS and HEME
# 5 coordenated iron.
bond REC.175.NE2 REC.293.FE
saveamberparm REC rec.1.leap.prm7 rec.1.leap.rst7
quit

$AMBERHOME/bin/tleap -s -f tleap.rec.1.in > ! tleap.rec.1.out

$AMBERHOME/bin/ambpdb -p rec.1.leap.prm7 < rec.1.leap.rst7 >! rec.1.leap.pdb

3.2 requires script 0000 to be run first and align/ dir to be present

reduce -HIS -FLIPs rec.1.leap.pdb >! rec.nowat.H_mod.pdb
sed -i 's/HETATM/ATOM  /g' rec.nowat.H_mod.pdb
grep "^ATOM  " rec.nowat.H_mod.pdb | sed -e 's/   new//g' | sed 's/   flip//g' | grep -v "OXT" | grep -v " 0......HEM" >! rec.nowat.H_mod1.pdb

curl docking.org/~tbalius/code/waterpaper2017/scripts/replace_his_with_hie_hid_hip.py > replace_his_with_hie_hid_hip.py
curl docking.org/~tbalius/code/waterpaper2017/scripts/replace_cys_to_cyx.py > replace_cys_to_cyx.py
curl docking.org/~tbalius/code/waterpaper2017/scripts/add.ters.py > add.ters.py

python replace_his_with_hie_hid_hip.py rec.nowat.H_mod1.pdb rec.nowat.H_mod2.pdb

The following script is useful if your protein has disulfides:

python replace_cys_to_cyx.py rec.nowat.H_mod2.pdb rec.nowat.H_mod3.pdb

output may be interted into the tleap input below to draw bonds. But this is not need here.

python add.ters.py rec.nowat.H_mod3.pdb rec.nowat.H_mod4.pdb

mv rec.nowat.H_mod4.pdb rec.nowat.H_final.pdb

(3.3) produces tleap input file (past on line at a time into your terminal, be sure not to have a space before the bottom EOF.

download HEME parameters:

curl docking.org/~tbalius/code/waterpaper2017/parms/frcmod_teb_mf_mod.hemall > frcmod_teb_mf_mod.hemall
curl docking.org/~tbalius/code/waterpaper2017/parms/heme_all_plus1.in > heme_all_plus1.in

cat << EOF >! tleap.rec.in
set default PBradii mbondi2
# load the protein force field
source leaprc.ff14SB
loadamberparams frcmod_teb_mf_mod.hemall
loadamberprep heme_all_plus1.in
REC = loadpdb rec.nowat.H_final.pdb
# draw bond between HIS and HEME
# 5 coordenated iron.
bond REC.175.NE2 REC.293.FE
XTALWAT = loadpdb wat.pdb
RECWAT  = combine {REC XTALWAT}
saveamberparm RECWAT rec.leap.prm7 rec.leap.rst7
solvateBox RECWAT TIP3PBOX 10.0
saveamberparm RECWAT rec.watbox.leap.prm7 rec.watbox.leap.rst7
quit
EOF

$AMBERHOME/bin/tleap -s -f tleap.rec.in > ! tleap.rec.out

Run AMBER

(1) Equilibrate

setenv LD_LIBRARY_PATH "/usr/local/cuda-6.0/lib64/:$LD_LIBRARY_PATH"

parmeters to add if writting in NetCDF

• ioutfm=1, write out NetCDF trajectory
• ntxo = 2, write out NetCDF restart
• ntrx = 2, read in NetCDF restart
• VMD does not read it in.
• half the size

cat << EOF1 > ! 01mi.in
01mi.in: equil minimization with Cartesian restraints
&cntrl
   imin=1, maxcyc=3000, ncyc = 1500,
   ntpr=100,
   ntr=1,
   restraint_wt=100.0,
   restraintmask= ':1-300 & !@H'
/
EOF1

cat << EOF1 > ! 02mi.in
02mi.in: equil minimization with Cartesian restraints
&cntrl
   imin=1, maxcyc=3000, ncyc = 1500,
   ntpr=100,
   ntr=1,
   restraint_wt=5.0,
   restraintmask= ':1-292 & !@H'
/
EOF1

cat << EOF1 > ! 01md.in
01md.in: equilibration, constant volume, constant temp at 50.00 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=0, ntx=1, nstlim = 10000,
   ntt=3, temp0=50.0, gamma_ln=2.0, ig = 1234,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 02md.in
02md.in: equilibration, constant volume, constant temp at 100.00 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 10000,
   ntt=3, temp0=100.0, gamma_ln=2.0, ig = 2345,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 03md.in
03md.in: equilibration, constant volume, constant temp at 150.00 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 10000,
   ntt=3, temp0=150.0, gamma_ln=2.0, ig = 3456,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 04md.in
04md.in: equilibration, constant volume, constant temp at 200.00 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 10000,
   ntt=3, temp0=200.0, gamma_ln=2.0, ig = 4567,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 05md.in
05md.in: equilibration, constant volume, constant temp at 250.00 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 10000,
   ntt=3, temp0=250.0, gamma_ln=2.0, ig = 5678,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 06md.in
06md.in: equilibration, constant volume, constant temp at 298.15 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 10000,
   ntt=3, temp0=298.15, gamma_ln=2.0, ig = 6789,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 07md.in
07md.in: equilibration, constant presure, constant temp at 298.15 run for 5ns (2500000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 2500000,
   ntt=3, temp0=298.15, gamma_ln=2.0, ig = 12345,
   ntp=1, taup=2.0,
   ntb=2, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

cat << EOF1 > ! 08md.in
08md.in: equilibration, constant volume, constant temp at 298.15 run for 5ns (2500000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 2500000,
   ntt=3, temp0=298.15, gamma_ln=2.0, ig = 23456,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

Make the file qsub.amber.equil.csh using vim (or your favorite text editor).

#$ -S /bin/csh
#$ -cwd
#$ -q gpu.q
#$ -o stdout
#$ -e stderr

# on-one-gpu is a used in the Shoichet lab for managing our gpus and may be removed. 
# setenv CUDA_VISIBLE_DEVICES "0,1,2,3"
setenv AMBERHOME /nfs/soft/amber/amber14/
set amberexe = "/nfs/ge/bin/on-one-gpu - \$AMBERHOME/bin/pmemd.cuda"

set filedir = `pwd`

# make a local directory on the server to run calculations
set SCRATCH_DIR = /scratch
if ! (-d $SCRATCH_DIR ) then
    SCRATCH_DIR=/tmp
endif
set username = `whoami`

set TASK_DIR = "\$SCRATCH_DIR/\${username}/$JOB_ID"
echo $TASK_DIR

mkdir -p ${TASK_DIR}
cd ${TASK_DIR}
pwd

cp ${filedir}/rec.watbox.leap.* .
cp ${filedir}/*.in . 

 $amberexe -O -i 01mi.in -o 01mi.out -p rec.watbox.leap.prm7 \
 -c rec.watbox.leap.rst7 -ref rec.watbox.leap.rst7 \
 -x 01mi.mdcrd -inf 01mi.info -r 01mi.rst7

 $amberexe -O -i 02mi.in -o 02mi.out -p rec.watbox.leap.prm7 \
 -c 01mi.rst7 -ref 01mi.rst7 \
 -x 02mi.mdcrd -inf 02mi.info -r 02mi.rst7

 # we should consider runing a step of NPT here first to at low temp to ajust the box size.
 # then swiching to fixed volume to rase the tempature.
 
 $amberexe -O -i 01md.in -o 01md.out -p rec.watbox.leap.prm7 \
 -c 02mi.rst7 -ref 02mi.rst7 -x 01md.mdcrd -inf 01md.info -r 01md.rst7

 # gzip 01md.mdcrd

 $amberexe -O -i 02md.in -o 02md.out -p rec.watbox.leap.prm7 \
 -c 01md.rst7 -ref 01md.rst7 -x 02md.mdcrd -inf 02md.info -r 02md.rst7

 $amberexe -O -i 03md.in -o 03md.out -p rec.watbox.leap.prm7 \
 -c 02md.rst7 -ref 01md.rst7 -x 03md.mdcrd -inf 03md.info -r 03md.rst7

 $amberexe -O -i 04md.in -o 04md.out -p rec.watbox.leap.prm7 \
 -c 03md.rst7 -ref 01md.rst7 -x 04md.mdcrd -inf 04md.info -r 04md.rst7

 $amberexe -O -i 05md.in -o 05md.out -p rec.watbox.leap.prm7 \
 -c 04md.rst7 -ref 01md.rst7 -x 05md.mdcrd -inf 05md.info -r 05md.rst7

 $amberexe -O -i 06md.in -o 06md.out -p rec.watbox.leap.prm7 \
 -c 05md.rst7 -ref 01md.rst7 -x 06md.mdcrd -inf 06md.info -r 06md.rst7

 $amberexe -O -i 07md.in -o 07md.out -p rec.watbox.leap.prm7 \
 -c 06md.rst7 -ref 01md.rst7 -x 07md.mdcrd -inf 07md.info -r 07md.rst7

 $amberexe -O -i 08md.in -o 08md.out -p rec.watbox.leap.prm7 \
 -c 07md.rst7 -ref 07md.rst7 -x 08md.mdcrd -inf 08md.info -r 08md.rst7

mv $TASK_DIR $filedir

qsub qsub.amber.produc1.csh

Wait for simulations to finish and then check the results. Make sure that 07md.in finished (this is when the box adjusts.

If 07md.in does not complete, run an additional step between 06md.in and 07md.in. Any error messages will be written in the "stderr" and "stdout" files.

cat << EOF1 > ! 07md_before.in
07md.in: equilibration, constant presure, constant temp at 298.15 run for 20ps (10000 steps).
&cntrl
   imin=0, irest=1, ntx=5, nstlim = 10000,
   ntt=3, temp0=298.15, gamma_ln=2.0, ig = 12345,
   ntp=1, taup=2.0,
   ntb=2, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-292 & !@H', restraint_wt = 5.0,
/
EOF1

Modify the above scripted as follows.

 $amberexe -O -i 06md.in -o 06md.out -p rec.watbox.leap.prm7 \
 -c 05md.rst7 -ref 01md.rst7 -x 06md.mdcrd -inf 06md.info -r 06md.rst7

 $amberexe -O -i 07md_before.in -o 07md_before.out -p rec.watbox.leap.prm7 \
 -c 06md.rst7 -ref 01md.rst7 -x 07md_before.mdcrd -inf 07md_before.info -r 07md_before.rst7

 $amberexe -O -i 07md.in -o 07md.out -p rec.watbox.leap.prm7 \
 -c 07md_before.rst7 -ref 01md.rst7 -x 07md.mdcrd -inf 07md.info -r 07md.rst7

(2) Production

cat << EOF1 > ! 09md.in
09md.in: production. constant volume, constant temp at 298.15 run for 5ns (2500000 steps).
&cntrl
   ioutfm=1, # write out NetCDF trajectory
   ntwr=1000000000,
   imin=0, irest=1, ntx=5, nstlim = 2500000,
   ntt=3, temp0=298.15, gamma_ln=2.0, ig = 34567,
   ntp=0, taup=2.0,
   ntb=1, ntc=2, ntf=2,
   ntwx=500, ntpr=500, dt = 0.002,
   ntr = 1, iwrap=1,
   restraintmask = ':1-290 & !@H', restraint_wt = 5.0,
/
EOF1

Make the file qsub.amber.produc1.csh using vim (or your favorite text editor).

#$ -S /bin/csh
#$ -cwd
#$ -q gpu.q
#$ -o stdout
#$ -e stderr

# on-one-gpu is a used in the Shoichet lab for managing our gpus and may be removed. 
# setenv CUDA_VISIBLE_DEVICES "0,1,2,3"
setenv AMBERHOME /nfs/soft/amber/amber14/
set amberexe = "/nfs/ge/bin/on-one-gpu - \$AMBERHOME/bin/pmemd.cuda"

set filedir = `pwd`

# make a local directory on the server to run calculations
set SCRATCH_DIR = /scratch
if ! (-d $SCRATCH_DIR ) then
    SCRATCH_DIR=/tmp
endif
set username = `whoami`

set TASK_DIR = "\$SCRATCH_DIR/\${username}/$JOB_ID"
echo $TASK_DIR

mkdir -p ${TASK_DIR}
cd ${TASK_DIR}
pwd

cp ${filedir}/rec.watbox.leap.* .
cp ../09md.in .
cp ../*/07md.rst7 . 
cp ../*/08md.rst7 .

cat 09md.in | sed 's/09md/10md/g' | sed 's/34567/10101/g'   > 10md.in
cat 09md.in | sed 's/09md/11md/g' | sed 's/34567/111/g'     > 11md.in
cat 09md.in | sed 's/09md/12md/g' | sed 's/34567/2121212/g' > 12md.in
cat 09md.in | sed 's/09md/13md/g' | sed 's/34567/131313/g'  > 13md.in
cat 09md.in | sed 's/09md/14md/g' | sed 's/34567/4443/g'    > 14md.in

 # stat production
 
 $amberexe -O -i 09md.in -o 09md.out -p rec.watbox.leap.prm7 \
 -c 08md.rst7 -ref 07md.rst7 -x 09md.mdcrd -inf 09md.info -r 09md.rst7

 $amberexe -O -i 10md.in -o 10md.out -p rec.watbox.leap.prm7 \
 -c 09md.rst7 -ref 07md.rst7 -x 10md.mdcrd -inf 10md.info -r 10md.rst7

 $amberexe -O -i 11md.in -o 11md.out -p rec.watbox.leap.prm7 \
 -c 10md.rst7 -ref 07md.rst7 -x 11md.mdcrd -inf 11md.info -r 11md.rst7

 $amberexe -O -i 12md.in -o 12md.out -p rec.watbox.leap.prm7 \
 -c 11md.rst7 -ref 07md.rst7 -x 12md.mdcrd -inf 12md.info -r 12md.rst7

 $amberexe -O -i 13md.in -o 13md.out -p rec.watbox.leap.prm7 \
 -c 12md.rst7 -ref 07md.rst7 -x 13md.mdcrd -inf 13md.info -r 13md.rst7

 $amberexe -O -i 14md.in -o 14md.out -p rec.watbox.leap.prm7 \
 -c 13md.rst7 -ref 07md.rst7 -x 14md.mdcrd -inf 14md.info -r 14md.rst7

mv $TASK_DIR $filedir

qsub qsub.amber.produc1.csh

After the above script finishes running on the gpu queue. Make sure all is in order and extend the simulation.

Make the file qsub.amber.produc2.csh using vim (or your favorite text editor).

#$ -S /bin/csh
#$ -cwd
#$ -q gpu.q
#$ -o stdout
#$ -e stderr

# on-one-gpu is a used in the Shoichet lab for managing our gpus and may be removed. 
# setenv CUDA_VISIBLE_DEVICES "0,1,2,3"
setenv AMBERHOME /nfs/soft/amber/amber14/
set amberexe = "/nfs/ge/bin/on-one-gpu - \$AMBERHOME/bin/pmemd.cuda"

set filedir = `pwd`

# make a local directory on the server to run calculations
set SCRATCH_DIR = /scratch
if ! (-d $SCRATCH_DIR ) then
    SCRATCH_DIR=/tmp
endif
set username = `whoami`

set TASK_DIR = "\$SCRATCH_DIR/\${username}/$JOB_ID"
echo $TASK_DIR

mkdir -p ${TASK_DIR}
cd ${TASK_DIR}
pwd

cp ${filedir}/rec.watbox.leap.* .
cp ../09.in .
cp ../*/07md.rst7 .
cp ../*/14md.rst7 . 

cat 09md.in | sed 's/09md/15md/g' | sed 's/34567/151515/g' > 15md.in
cat 09md.in | sed 's/09md/16md/g' | sed 's/34567/161616/g' > 16md.in
cat 09md.in | sed 's/09md/17md/g' | sed 's/34567/171717/g' > 17md.in
cat 09md.in | sed 's/09md/18md/g' | sed 's/34567/181818/g' > 18md.in

 # extend production
 
 \$amberexe -O -i 15md.in -o 15md.out -p rec.watbox.leap.prm7 \
 -c 14md.rst7 -ref 07md.rst7 -x 15md.mdcrd -inf 15md.info -r 15md.rst7

 \$amberexe -O -i 16md.in -o 16md.out -p rec.watbox.leap.prm7 \
 -c 15md.rst7 -ref 07md.rst7 -x 16md.mdcrd -inf 16md.info -r 16md.rst7

 \$amberexe -O -i 17md.in -o 17md.out -p rec.watbox.leap.prm7 \
 -c 16md.rst7 -ref 07md.rst7 -x 17md.mdcrd -inf 17md.info -r 17md.rst7

 \$amberexe -O -i 18md.in -o 18md.out -p rec.watbox.leap.prm7 \
 -c 17md.rst7 -ref 07md.rst7 -x 18md.mdcrd -inf 18md.info -r 18md.rst7

mv \$TASK_DIR $pwd 

(3) Restart

Some times the simulation will fail to run properly, so you may have to restart it.

Run GIST post processing

(0) make symbolic links to all the trajectory files.

set list = "4953439 4953257"
foreach dir ($list) 
  ln -s $dir/*mdcrd .
  ln -s $dir/*md.rst7 .
end

or if you do not want to specify the directory names:

 ln -s */*mdcrd .
 ln -s */*md.rst7 .

(1) make a reference frame from the simulation.

cat << EOF >! makeref.in 
parm rec.watbox.leap.prm7 
# 10md.rst7 is the start of the second 5 ns of production
trajin 10md.rst7 1 1 
strip :WAT
trajout ref.pdb pdb
go
EOF

/nfs/soft/amber/amber14/bin/cpptraj -i makeref.in > ! makeref.log &

(2) align the ligand to the MD frame and calculate the center of mass.

set mountdir = `pwd`

set workdir = $mountdir/align

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

get the right files.

set file1 = "../ref.pdb"
set file2 = "../rec.pdb"
set file3 = "../xtal-lig.pdb" 
set file4 = "../waters.pdb" 

write the chimera commands to align things.

cat << EOF > chimera.com
# template #0
open $file1 
# rec #1
open $file2 
# xtal-lig
open $file3 
# waters
open $file4 
# move original to gist. it is harder to move the gist grids. 
mmaker #0 #1 
matrixcopy #1 #2
matrixcopy #1 #3

write format pdb   0 template.pdb
write format pdb   1 aligned.rec.pdb
write format pdb   2 aligned.lig.pdb
write format mol2  2 aligned.lig.mol2
write format pdb   3 aligned.waters.pdb
EOF

set chimerapath = "/nfs/soft/chimera/current/bin/chimera"

${chimerapath} --nogui chimera.com > & chimera.com.out

curl http://docking.org/~tbalius/code/for_dock_3.7/mol2.py > mol2.py
curl http://docking.org/~tbalius/code/for_dock_3.7/mol2_center_of_mass.py > mol2_center_of_mass.py

python mol2_center_of_mass.py aligned.lig.mol2 centermol.txt

(3) run cpptraj to calculate the GIST grids.

set mountdir = `pwd`

set workdir = $mountdir/full_gist

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

ln -s $mountdir/rec.watbox.leap.prm7 .
ln -s $mountdir/09md.mdcrd .
ln -s $mountdir/10md.mdcrd .
ln -s $mountdir/11md.mdcrd .
ln -s $mountdir/12md.mdcrd .
ln -s $mountdir/13md.mdcrd .
ln -s $mountdir/14md.mdcrd .
ln -s $mountdir/15md.mdcrd .
ln -s $mountdir/16md.mdcrd .
ln -s $mountdir/17md.mdcrd .
ln -s $mountdir/18md.mdcrd .
ln -s $mountdir/align/centermol.txt .

get center of grid from aligned.lig.pdb

set center = `cat centermol.txt`

cat << EOF >! gist.in
parm rec.watbox.leap.prm7 
trajin 09md.mdcrd 1 10000
trajin 10md.mdcrd 1 10000
trajin 11md.mdcrd 1 10000  
trajin 12md.mdcrd 1 10000 
trajin 13md.mdcrd 1 10000 
trajin 14md.mdcrd 1 10000 
trajin 15md.mdcrd 1 10000 
trajin 16md.mdcrd 1 10000 
trajin 17md.mdcrd 1 10000
trajin 18md.mdcrd 1 10000
gist doorder refdens 0.0329 gridcntr $center griddim 40 40 40 gridspacn 0.50 out gist.out
go
EOF 

make sure there is no space before the "EOF" end of file designator.

We can change the box dimensions form 40 40 40 to, say 45 45 55, to elongate the box in the z direction.

refdens refers to the bulk number density for the water model used during the MD simulation. Use 0.0329 if you ran your simulation with TIP3P waters. Consult the Amber manual for other Amber water number densities.

cat << EOF > qsub.csh
#\$ -S /bin/csh
#\$ -cwd
#\$ -q all.q
#\$ -o stdout
#\$ -e stderr

cd $workdir

/nfs/soft/amber/amber14/bin/cpptraj -i gist.in > ! gist.log

EOF

make sure there is no space before the "EOF" end of file designator.

Now let us submit the script to the queue so run the script on a node on our cluster.

qsub qsub.csh

If want to run this on the current machine (front end node) then replace "qsub" with "csh".

Combining GIST grids

You may use the following python tools for combining GIST grids:

wget https://github.com/tbalius/GIST_DX_tools/archive/master.zip
unzip master.zip

This creating a directory called GIST_DX_tools-master.

set mountdir = `pwd`
set workdir = "${mountdir}/combined_gist_grids"
set filedir = "${mountdir}"

rm -rf  ${workdir}
mkdir ${workdir}
cd ${workdir}

cp $filedir/gist-dTSorient-dens.dx .
cp $filedir/gist-dTStrans-dens.dx .
cp $filedir/gist-Esw-dens.dx .
cp $filedir/gist-Eww-dens.dx .

The following constants were obtained from the amber manual:

-9.533 * 0.0334 = -0.3184 and  2* 0.3184 = 0.6368

Note that the 0.6368 is positive. This is because we are subtracting -0.3184.

If you are using a different solvent model, consult the Amber manual for the correct water-water mean energy and water number density, e.g. for TIP4PEw:

-11.036 * 0.0332 = -0.3663952 and 2* 0.3663952 = 0.7327904

The old (amber 12) and new grids (amber 14) differ by a factor of 2 in the water-water enthalpy grid.

 python ../GIST_DX_tools-master/src/dx-combine_grids.py gist-Eww-dens.dx 2.0 gist-gO.dx 0.6368 0.0 gist-dEww-dens_ref2
 python ../GIST_DX_tools-master/src/dx-combine_grids.py gist-Esw-dens.dx 1.0 gist-dEww-dens_ref2.dx 1.0 0.0 gist-EswPlusEww_ref2
 python ../GIST_DX_tools-master/src/dx-combine_grids.py gist-EswPlusEww_ref2.dx 1.0 gist-TSsw.dx -1.0 0.0 gist-Gtot_ref2

 python ../GIST_DX_tools-master/src/dx-combine_grids.py gist-Eww-dens.dx 1.0 gist-gO.dx 0.3184 0.0 gist-dEww-dens_ref
 python ../GIST_DX_tools-master/src/dx-combine_grids.py gist-Esw-dens.dx 1.0 gist-dEww-dens_ref.dx 1.0 0.0 gist-EswPlusEww_ref
 python ../GIST_DX_tools-master/src/dx-combine_grids.py gist-EswPlusEww_ref.dx 1.0 gist-TSsw.dx -1.0 0.0 gist-Gtot_ref

insert a figure

Run convergence analysis

Write the following in a script called cpptraj_subtraj.csh:

set mountdir = `pwd`

#set center = `grep N3 /mnt/nfs/work/tbalius/Water_Project_newgrid_mod2_heme_charge/workingdir/align_CYTc_B/aligned.lig.pdb | awk '{print $7" "$8" "$9}'`
set center = `cat $mountdir/align/centermol.txt`

foreach traj ( \
 09md \
 10md \
 11md \
 12md \
 13md \
 14md \
 15md \
 16md \
 17md \
 18md \
)

cd $mountdir

rm -r ${traj}_gist
mkdir ${traj}_gist
cd ${traj}_gist

set workdir = $mountdir/${traj}_gist

ln -s $mountdir/rec.watbox.leap.prm7 .
ln -s $mountdir/$traj.mdcrd .

cat << EOF >! gist.$traj.in
 parm rec.watbox.leap.prm7 
 trajin $traj.mdcrd 1 10000
 gist doorder doeij gridcntr $center griddim 45 45 55 gridspacn 0.50 out gist.out
 go
EOF # make sure there is no space before EOF
#gist doorder refdens 0.0329 gridcntr 35.759163 33.268703 31.520596 griddim 40 40 40 gridspacn 0.50 out gist.out

cat << EOF > qsub.csh
#\$ -S /bin/csh
#\$ -cwd
#\$ -q all.q
#\$ -o stdout
#\$ -e stderr

cd $workdir

/nfs/soft/amber/amber14/bin/cpptraj -i gist.$traj.in > ! gist.$traj.log 

EOF # make sure there is no space before EOF
qsub qsub.csh

end # traj

Combine each chunk as we did above in the combine section with the following script:

#!/bin/csh 

set mountdir = `pwd`

foreach subtraj ( \
 09md \
 10md \
 11md \
 12md \
 13md \
 14md \
 15md \
 16md \
 17md \
 18md \
)


set workdir = $mountdir/gist_grids/$subtraj
set filedir = "$mountdir/${subtraj}_gist"

rm -rf  ${workdir}
mkdir ${workdir}
cd ${workdir}

cp $filedir/gist-dTSorient-dens.dx .
cp $filedir/gist-dTStrans-dens.dx .
cp $filedir/gist-Esw-dens.dx .
cp $filedir/gist-Eww-dens.dx .

# this is the density of the water.
cp $filedir/gist-gO.dx .


cat <<EOF > qsub.csh
#!/bin/csh 
#\$ -cwd
#\$ -j yes
#\$ -o stderr
#\$ -q all.q

 cd ${workdir}
 #make a combination of the grids
 # We think that we should be substracting
 # Remove comment from top of line
 
 # echo "scale=2; -9.533 * 0.0334 " | bc
 # -0.3184 should be positive -*- = +
 # 2* 0.3184 = 0.6368
 # the old and new grids differ by a factor of 2. 

  python ~/zzz.scripts/dx-combine_grids.py gist-Eww-dens.dx 2.0 gist-gO.dx 0.6368 0.0 gist-dEww-dens_ref2

  python ~/zzz.scripts/dx-combine_grids.py gist-Esw-dens.dx 1.0 gist-dEww-dens_ref2.dx 1.0 0.0 gist-EswPlusEww_ref2

EOF

#qsub qsub.csh 
csh qsub.csh 



end # subtraj

Now lets generated plots:

#!/bin/csh 

set mountdir = `pwd` 
set mountdir2 = ${mountdir}/gist_grids/

#set type = "gist-gO"
#set type = "gist-EswPlusEww_ref2"
#set type = "gist-Esw-dens"
#set type = "gist-Eww-dens"
set type = "gist-dEww-dens_ref2"


set oldtraj = "" # set it to nothing, it is updated in the for loop. 
 
set workdir = "${mountdir2}/${type}_conv"
rm -rf $workdir
mkdir -p $workdir
cd $workdir

foreach traj ( \
 09md \
 10md \
 11md \
 12md \
 13md \
 14md \
 15md \
 16md \
 17md \
 18md \
)

  if ($traj != "09md") then
       python ~/zzz.scripts/dx-compare_2norm.py ${mountdir2}/${oldtraj}/${type}.dx ${mountdir2}/${traj}/${type}.dx ${oldtraj}_${traj}_diff >! ${oldtraj}_${traj}_diff.log
  endif
  
  ls -l ${mountdir2}/${type}.dx  ${mountdir2}/${traj}/${type}.dx full_${traj}_diff
  python ~/zzz.scripts/dx-compare_2norm.py  ${mountdir2}/${type}.dx  ${mountdir2}/${traj}/${type}.dx full_${traj}_diff  >! full_${traj}_diff.log
  python ~/zzz.scripts/dx-compare_2norm.py ${mountdir2}/${traj}/${type}.dx ${mountdir2}/gist-zero.dx ${type}_${traj}_zeros_diff >! ${type}_${traj}_zeros_diff.log
  set oldtraj = $traj
end # traj

python ~/zzz.scripts/dx-compare_2norm.py ${mountdir2}/${type}.dx ${mountdir2}/gist-zero.dx ${type}_${traj}_zeros_diff >! ${type}_full_zeros_diff.log

#cd ${mountdir}