# grep -v means "everything but" last grep statement removes inconsistently named HEM hydrogens (for leap to be added back in) $DOCKBASE/proteins/Reduce/reduce -HIS -FLIPs rec.1.leap.pdb >! $AMBERHOME/bin/ambpdb -p rec.1.leap.prm7 ! rec.1.leap.pdb $AMBERHOME/bin/tleap -s -f tleap.rec.1.in > ! tleap.rec.1.out # runs tleap and converts parameter and coordinate restart file back into pdb file Saveamberparm REC rec.1.leap.prm7 rec.1.leap.rst7 # draw bond between HIS and HEME with 5 coordinated iron. # produces tleap input file - renumbers rec # 1st: run leap just to renumber residues. #cp $filedir/nearby_waters_aligned.pdb wat.pdbĬurl /~tbalius/code/waterpaper2017/parms/frcmod_teb_mf_mod.hemall > frcmod_teb_mf_mod.hemallĬurl /~tbalius/code/waterpaper2017/parms/heme_all_plus1.in > heme_all_plus1.in # uncomment the next line to include Xtal waters into simulation #set mountdir = "/mnt/nfs/work/tbalius/Water_Project/run_DOCK3.7" #set list = `cat /nfs/work/users/tbalius/VDR/Enrichment/pdblist_rat ` # setenv AMBERHOME /nfs/soft/amber/amber14 # This script runs beblasti, creates dirs and splits pdb into rec and lig file for running amber MD. Write the following script, named 001md.be_balsti_reduce.csh, using your favorate text editor (like vim). Set path = ( /nfs/home/tbalius/zzz.programs/msms $path ) Setenv DOCKBASE "/nfs/home/tbalius/zzz.github/DOCK" Source /nfs/soft/python/envs/complete/latest/env.csh
You can add the following to your environment file (.cshrc) for just issue them on the command line. Here, we will use these grids for DOCKing (although, there are many other uses). Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodynamic properties of water on GIST lattice. It is helpful if you have DOCK3.7 the latest version.In our case we uses an SGE queuing system to manage these jobs. To use this tutorial you will need the following: But we hope that the community finds this useful. This is foremost for training Shoichet lab members.
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