-
拆分对接结果
vina_split --input result.pdbqt --ligand complex/lig
-
使用mv命令批量修改文件名，把01-09修改成1-9，便于批量处理
for i in `seq 1 9`; do
> mv "lig0${i}.pdbqt" "lig${i}.pdbqt"
> done
- 使用Openbabel把pdbqt转成pdb
for i in `seq 1 20`; do
> obabel -ipdbqt lig${i}.pdbqt -opdb -O lig${i}.pdb
> done
- 使用cat命令把ligand.pdb和receptor.pdb合成为complex.pdb
for i in `seq 1 20`; do
> cat ../ev71_none_2mer.pdb lig${i}.pdb > complex${i}.pdb
> done
- 使用freesasa计算接触面积
recptor:freesasa ev71_none_2mer.pdb -n 100 --depth=residue -o sasa/rec
ligand:
for i in `seq 1 20`; do
> freesasa complex/lig${i}.pdb -n 100 -H --depth=residue -o sasa/lig${i}
> done
complex:
for i in `seq 1 20`; do
> freesasa complex/complex${i}.pdb -n 100 -H --depth=residue -o sasa/complex${i}
> done
接触面积的计算公式为：(rec_sasa + lig_sasa - complex_sasa) / 2
# 切换到tag工作文文件夹
os.chdir('/data5_large/home/xyli/enterovirus/ev71-tag/docking/none/vina')# 配体ev71的sasa
with open('./sasa/rec', 'r') as rec_log:text = rec_log.readlines()total = text[15]
rec_sasa = eval(total[10:].lstrip())inter_sasa_ls = []
for i in range(1,21):# 依次读取每个lig的sasalig_file = 'lig%d'%iwith open(f'./sasa/{lig_file}', 'r') as lig_log:text = lig_log.readlines()total = text[15]lig_sasa = eval(total[10:].lstrip())# 依次读取每个复合物的sasacomplex_file = 'complex%d'%iwith open(f'./sasa/{complex_file}', 'r') as complex_log:text = complex_log.readlines()total = text[15]complex_sasa = eval(total[10:].lstrip())# 计算binding areainter_sasa = (rec_sasa+lig_sasa-complex_sasa)/2inter_sasa_ls.append(inter_sasa)
