1226 HSP90 SMD

概述

# CV设置为关键氨基酸的主链
# 对蛋白主链施加位置限制
85.24 /home/databank/zzy/project/MD/koff/smd/cv-res_bb-mol-restbb-0918


85.23 /home/databank_70t/zzy/project/koff/smd/hsp90/test1/2uwd/test1

CV

/home/databank_70t/zzy/project/koff/smd/hsp90/cv
# pymol 里看关键氨基酸
2uwd：r36|r78|r82|r169
2yki：r35|r77|r123|r168
5j2x：r33|r43|r78|r82|r169
5j64：r36|r43|r78|r82|r169
5odx：r36|r37|r78|r82
5t21：r38|r77|r123|r168
6eln：r77|r81|r168
6eyb：r77

SMD

# 85.23 /home/databank_70t/zzy/project/koff/smd/hsp90/test1
# gmx pull code 如果牵引距离大于盒子的一半，会报错，倒是无伤大雅，过一段时间会自动退出
nohup sh smd.sh &
###################### "smd.sh" 33L, 714C ##########################################
for i in `awk '{print $1}' 8sys-cv`
do
a=`grep -w $i 8sys-cv|awk '{print $2}'`
b=`grep -w $i 8sys-cv|awk '{print $2}'|sed 's/|/_/g'|sed 's/r/r_/g'`


echo $i $a $b


(echo "$a"; echo 'q') | gmx_mpi make_ndx -f $i/npt.gro -o $i/index.ndx


echo 4 | gmx_mpi genrestr -f $i/npt.gro -o $i/posre.itp


sed "s/KEY_RESN/$b/g" smd.mdp >$i/smd.mdp


gmx_mpi grompp -f $i/smd.mdp -p $i/gromacs.top -c $i/npt.gro -r $i/npt.gro -n $i/index.ndx -o $i/smd.tpr -maxwarn 1


cd $i
for c in {1..5}
do
mkdir -p $c
cd $c
cp ../smd.tpr ./
mpirun -np 100 gmx_mpi mdrun -v -deffnm smd
cd ../
done


cd ../
done
###################### 12-26 21：16 #################################################

2yki/npt.gro:  122PHE    CE1 1881   3.350   3.404   3.442 -0.2550  0.2030  0.0911
5t21/npt.gro:  122PHE    CE1 1881   3.010   3.393   3.255 -0.2112  0.7167 -0.4057

轨迹分析

可视化+统计Fmax

# 可视化轨迹
# 效果挺好
nohup sh smd.sh &
sz */*/look*
########################### "smd.sh" 16L, 282C ######################################
for i in `awk '{print $1}' 8sys-cv`
do
cd $i
(echo '1|13'; echo 'q') | gmx_mpi make_ndx -f npt.gro -o index2.ndx


echo "############ $i ############"
for c in {1..5}
do
cd $c
echo 21|gmx_mpi trjconv -f smd.xtc -s smd.tpr -n ../index2.ndx -o look${i}-${c}.pdb -pbc mol -ur compact -skip 100
sort -g -k2nr smd_pullf.xvg |head -n1|awk '{print $2}'
cd ../
done


cd ../
done
####################################################################################

Fmax