| cpuhyy |
2009-04-13 17:49 |
一个中间路线就是用gromacs跑轨迹，用autodock算能量（自由能），虽然不如mmpbsa原理上准确，但是忽略部分熵效应也在变动不大的体系也还不错。下面这个脚本,可以实现这一功能，希望能对大家有个帮助：（脚本高手可以看看是否有用，仅供参考）
#!/bin/sh
#'$1' is set for different list name
#'$2' is set for the ligand name
#prepare the $2.bnd in advance with command:
#/~root/autodock/dist305/bin/pdbtoatm lig.pdbq| ~root/autodock/dist305/bin/atmtobnd >lig.bnd for snapshot in `cat $1` do rec=protein_mn_hoh1.${snapshot} lig=$2.${snapshot} echo ${rec}
#assign the atomic solvation parameters to PDBQ-formatted version of your macromolecule, ~root/bin/addsol ${rec}.pdbq ${rec}.pdbqs ~root//bin/autotors -A $2.bnd ${lig}.pdbq ${lig}.out.pdbq > ${lig}.out.${rec}.epdb.com ~root/autodock/dist305/bin/autodock3 -p ${lig}.out.${rec}.dpf -l ${lig}.out.${rec}.epdb.log -c > $1_Binding ~root//bin/Docked.awk ${lig}.out.${rec}.epdb.log >> $1_Docked ~root//bin/Inter_score.awk ${lig}.out.${rec}.epdb.log >> $1_Inter_Energy ~root//bin/Intra_score.awk ${lig}.out.${rec}.epdb.log >> $1_Intra_Energy #rm -f *.map *.fld *.xyz *.err *.pdbqs *.glg *.log *.com *.gpf *.dpf Binding.awk
#!~root/bin/gawk -f BEGIN{ name=ARGV[1] split(name,array,".") } { if($0 ~ /Estimated Free Energy of Binding/) {print array[1]" "$9" " $10} } Docked.awk
#!~root/bin/gawk -f BEGIN{ name=ARGV[1] split(name,array,".") } { if($0 ~ /Final Docked Energy/) {print array[1]" "$7" " $8} } |
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