4zy4配体

conda activate ambertools
tleap


source leaprc.gaff2  
source leaprc.water.opc 


loadamberparams /home/lywu/pengziyu/0103/t28-2/lig_4zy4-t28.frcmod
loadamberprep /home/lywu/pengziyu/0103/t28-2/lig_4zy4-t28.prep


mol = loadpdb /home/lywu/pengziyu/0103/t28-2/lig_4zy4-t28.pdb


saveamberparm mol lig.prmtop lig.inpcrd
savepdb mol mol-dry.pdb


charge mol
solvatebox mol OPCBOX 12
addionsrand mol Cl- 1


saveAmberParm mol complex.prmtop complex.inpcrd
savePdb mol complex.pdb
quit

# AMBER 参数转 GMX 参数
#进入python 
import parmed as pmd
amber = pmd.load_file('complex.prmtop','complex.inpcrd')
amber.save('gmx.top')
amber.save('gmx.gro')

; Include Position restraint file
 #ifdef  POSRES
 #include "posre1.itp

source ~/.gmx2022.5-remd.sh
gmx_mpi genrestr -f gmx.gro -o posre1.itp

mkdir pre-equ
mkdir em nvt npt mdp
cp /home/databank/lywu/vsremd_plus/protein-ligand/trypsin-benzamidine/pre-equilibrium/mdp-file/* ./mdp/
cp ../gmx.gro ./


### 能量最小化 在em/
gmx_mpi grompp -f ../mdp/em.mdp -c ../gmx.gro -r ../gmx.gro -p ../gmx.top -o em.tpr 
nohup gmx_mpi mdrun -v -deffnm em &


### 等温等容预平衡 在nvt/
gmx_mpi grompp -f ../mdp/nvt.mdp -c .G./em/em.gro -r ../em/em.gro -p ../gmx.top -o nvt.tpr
nohup mpirun -np 100 gmx_mpi mdrun -v -deffnm nvt &


### 等温等压预平衡 在npt/
gmx_mpi grompp -f ../mdp/npt.mdp -c ../nvt/nvt.gro -r ../nvt/nvt.gro -p ../gmx.top -o npt.tpr
nohup mpirun -np 100 gmx_mpi mdrun -v -deffnm npt &