Qnifft compile, run: Difference between revisions

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(Created page with "**************** COMPILE *************************** 1. ssh <user>@psi 2. export path = /nfs/soft/pgi/current/linux86-64/12.10/bin 3. source /nfs/soft/pgi/env.csh 4. cd $D...")
 
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**************** COMPILE ***************************
COMPILE


1. ssh <user>@psi
ssh <user>@psi


2. export path = /nfs/soft/pgi/current/linux86-64/12.10/bin
export path = /nfs/soft/pgi/current/linux86-64/12.10/bin


3. source /nfs/soft/pgi/env.csh
source /nfs/soft/pgi/env.csh


4. cd $DOCKBASE/proteins/qnifft/src/source/qnifft/v2.2/
cd $DOCKBASE/proteins/qnifft/src/source/qnifft/v2.2/


5. make clean
make clean


6. make
make








************** USAGE *******************************
USAGE


1. change the qnifft.parm


2. /nfs/home/enkhjargal/Docking/dock3.7/DOCK_GNU/DOCK/proteins/qnifft/src/source/qnifft/v2.2/qnifft22_289_pgf_64 qnifft.parm
change the qnifft.parm


3. cp /mnt/nfs/work/rstein/REC_DESOLV_test/convert_phi_to_dx.py .
/nfs/home/enkhjargal/Docking/dock3.7/DOCK_GNU/DOCK/proteins/qnifft/src/source/qnifft/v2.2/qnifft22_289_pgf_64 qnifft.parm


4. python convert_phi_to_dx.py qnifft.electrostatics.phi qnifft.dx
cp /mnt/nfs/work/rstein/REC_DESOLV_test/convert_phi_to_dx.py .


5. /nfs/soft/chimera/current/bin/chimera receptor.crg.lowdielectric.pdb qnifft.dx
python convert_phi_to_dx.py qnifft.electrostatics.phi qnifft.dx


6. python ~tbalius/zzz.github/DOCK/proteins/blastermaster/phiTrim.py qnifft.electrostatics.phi box trim.electrostatics.phi
/nfs/soft/chimera/current/bin/chimera receptor.crg.lowdielectric.pdb qnifft.dx
 
python ~tbalius/zzz.github/DOCK/proteins/blastermaster/phiTrim.py qnifft.electrostatics.phi box trim.electrostatics.phi

Latest revision as of 18:43, 30 November 2016

COMPILE

ssh <user>@psi
export path = /nfs/soft/pgi/current/linux86-64/12.10/bin
source /nfs/soft/pgi/env.csh
cd $DOCKBASE/proteins/qnifft/src/source/qnifft/v2.2/
make clean
make



USAGE


change the qnifft.parm
/nfs/home/enkhjargal/Docking/dock3.7/DOCK_GNU/DOCK/proteins/qnifft/src/source/qnifft/v2.2/qnifft22_289_pgf_64 qnifft.parm
cp /mnt/nfs/work/rstein/REC_DESOLV_test/convert_phi_to_dx.py .
python convert_phi_to_dx.py qnifft.electrostatics.phi qnifft.dx
/nfs/soft/chimera/current/bin/chimera receptor.crg.lowdielectric.pdb qnifft.dx
python ~tbalius/zzz.github/DOCK/proteins/blastermaster/phiTrim.py qnifft.electrostatics.phi box trim.electrostatics.phi