lingyuzeng/gromacs_docker
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

add all

Browse Source
This commit is contained in:
root
2024-09-26 16:39:11 +08:00
parent 111de00dd5
commit bf2b289c67
18 changed files with 488 additions and 4 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
script/S112D/S112D.sh
View File

@@ -9,7 +9,7 @@ if [ -n "$GMXRC_PATH" ]; then
source "$GMXRC_PATH" # source /home/lingyuzeng/software/gmx2023.2/bin/GMXRC
fi
GPU_ID=${GPU_ID:-"0"}
NAME=${NAME:-"S112D-Alphafold2"}
LIGAND_GRO="ligand.gro" # 配体的 .gro 文件
LIGAND_ITP="ligand.itp" # 配体的 .itp 文件
# FORCEFIELD=${FORCEFIELD:-"amber99sb-ildn"}
@@ -57,13 +57,15 @@ echo "EXTRACT_EVERY_PS: $EXTRACT_EVERY_PS"
# Step 1: Generate GROMACS .gro file for the protein
gmx_mpi pdb2gmx -f $NAME.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -p topol.top -ignh
# gmx_mpi pdb2gmx -f protein.pdb -o protein.gro -ff $FORCEFIELD -water $WATERMODEL -p topol.top -ignh
# gmx_mpi pdb2gmx -f protein.pdb -o $NAME.gro -ff $FORCEFIELD -water $WATERMODEL -p topol.top -ignh
# gmx_mpi pdb2gmx -f protein.pdb -o protein.gro -ff amber99sb -water tip3p -p unk.top -ignh
# 使用 Sobtop（http://sobereva.com/soft/Sobtop）提取
# Step 2: Merge protein and ligand .gro files into a complex
cat protein.gro mol.gro > complex.gro
cat $NAME.gro mol.gro > complex.gro
# 获取蛋白质和小分子的原子数
PROTEIN_ATOMS=$(head -n 2 protein.gro | tail -n 1 | tr -d ' ')
PROTEIN_ATOMS=$(head -n 2 $NAME.gro | tail -n 1 | tr -d ' ')
LIGAND_ATOMS=$(head -n 2 mol.gro | tail -n 1 | tr -d ' ')
# 打印原子数，确保正确