轨迹分析（5sys+2active)

The results are presented in three parts: (i) the “Dynamic Behavior of Complexes” section, which discusses RMSD and RMSF analyses; (ii) the “Predicted Highly Frequent Residues of Ligand Binding” section, which examines the interaction frequencies between ligands and key residues; and (iii) the “Essential Residues in Protein–Ligand Binding” section, which uses MM/GBSA calculations to identify critical binding residues.

周期性处理

# GMX -pbc nojump -ur compact + -fit rot+trans
# 除 91433-17-9 外的4个体系工作路径为 /home/dddc/zyzhou/project/hsbd/2025-4bioactive/cmd/analysis/periodic-processing
# 91433-17-9 与两个阳性化合物工作路径为

RMSD

75.3 /home/dddc/zyzhou/project/hsbd/2025-4bioactive/cmd/analysis/rmsd
scp dddc@172.21.85.23:/home/databank_70t/zzy/project/hsbd/2024-pl-13mol/analysis/rmsd/complex/* ./
# 之前有写过脚本，可直接使用，需要修改路径
# 作图脚本需要逐行检查
# 已出图，没问题


# 75.3  /home/dddc/zyzhou/project/hsbd/2025-4bioactive/cmd/analysis/rmsd
# 补充了蛋白RMSD和配体RMSD的计算，还没画图

RMSF

75.3 /home/dddc/zyzhou/project/hsbd/2025-4bioactive/cmd/analysis/rmsf
cp ../rmsd/* ./
# 与rmsd的脚本逻辑几乎完全一致，rmsf的gmx计算命令稍有不同，修改即可
# 作图脚本需要逐行检查


# RMSF是根据残基计算的（-res),在处理双链时需要注意，两条链需要分开处理
# 本身也是很有意思的信息，双链RMSF波动的区别可以一定程度上反应配体的结合吗？


# 看了一下，两条链中差距不算大
# 分别做了两条链按照残基取平均的结果和比较每次平行实验两条链RMSF的图


# 二聚体处理示例
# 正常运行脚本后，将两条链的数据拆分，按行合并
cp 91433-17-9-dock-PL_rmsf.xvg chain2.xvg
paste -d ',' 91433-17-9-dock-PL_rmsf.xvg chain2.xvg >91433-17-9-dock-PL_rmsf-dimer.xvg


awk -F',' 'NR==1 {print $1","$2","$3","$4} NR>1 {avg2=($2+$6)/2; avg3=($3+$7)/2; avg4=($4+$8)/2; printf "%.3f,%.3f,%.3f,%.3f\n", $1, avg2, avg3, avg4}' 91433-17-9-dock-PL_rmsf-dimer.xvg > 91433-17-9-dock-PL_rmsf-dimer-average.xvg


# 两条链取平均后，三次实验再取平均的图（简单说明体系稳定）还没做

MM/GBSA

85.23 /home/databank_70t/zzy/project/hsbd/2025-4bioactive/analysis/mmgbsa
(base) [dddc@localhost workdir]$ nohup bash mmgbsa-cal.sh &
[1] 213572
# 已在23上提交任务 18：28


# 尝试在75.3上安装amber24
# /home/dddc/zyzhou/software/amber24/amber24_src
# ./update_amber --update 已完成 18：32


# 想与老师们讨论：当受体结构不同，结合位点差异较大时，结合自由能的比较是否有意义？

Frequencies of interaction + resn dG contribution

distance-name-resi.ipynb

75.3 /home/dddc/zyzhou/project/hsbd/2025-4bioactive/cmd/analysis/Frequencies_of_interaction
##################################### do.sh #################################################
for i in {1..5}
do 
a=`sed -n "${i}p" index|awk -F ',' '{print $1}'`
b=`sed -n "${i}p" index|awk -F ',' '{print $2}'`
echo "####### $a $b #######"
for x in {1..3}
do 
mkdir -p $a


echo 18|gmx_mpi trjconv -s ../../../cmd/100ns/$a/md.tpr -f ../periodic-processing/$a/pbc-fit-${x}.xtc -n ../periodic-processing/$a/index.ndx -o $a/ref-${x}.pdb -dump 0


python cal-min_dis_between_lig_resn.py -p $a/ref-${x}.pdb -f ../periodic-processing/$a/pbc-fit-${x}.xtc -n $b -t 100002 --title "Minimum Distance of $a" -O ${a}-exp${x}.png


mv heavyatom_mindist $a/heavyatom_mindist-exp${x}
mv ${a}-exp${x}.png $a


done
done
##############################################################################################

mmgbsa-decomposition

# 23 /home/databank_70t/zzy/project/hsbd/2025-4bioactive/analysis/mmgbsa/decomposition/v2
for i in `cat sys`;do python draw.py -i data/${i}-key-res.txt -o decomposition-fig/${i}.png;done