0108 4zy4-t28 第三次实验

antechamber -i docking_4zy4-t28.sdf -fi sdf -o lig.gjf -fo gcrt -at gaff2 -gn "%nproc=4" -gm "%mem=4GB" -gk "#B3LYP/6-31G* em=gd3bj pop=MK iop(6/33=2,6/42=6) opt" -rn MOL  -nc 1
nohup g16 lig.gjf &
antechamber -i lig.log -fi gout -o lig.prep -fo prepi -c resp;parmchk2 -i lig.prep -f prepi -o lig.frcmod -a y


dos2unix *
grep -v "CONECT" gv-NEWPDB.pdb |cut -b 1-26 > symbol
cat gv-docking-4zy4.pdb | cut -b 29-78|sed '1,2d'|sed '1i Combineing the coordinates from the crystal structure with the atomic numbers from the Gaussian optimized structure'> coordinate
paste -d " " symbol coordinate|sed '1i TITLE      lig_4zy4-t28.pdb'> lig_4zy4-t28.pdb


conda activate pdb2pqr
pdb2pqr30 docking_4zy4_pre.pdb 4zy4.pqr --ff AMBER --ffout AMBER --with-ph 7.4 --pdb-output 4zy4_pred.pdb

conda activate ambertools
tleap
source leaprc.protein.ff19SB
source leaprc.gaff2  
source leaprc.water.opc


loadamberparams "/home/lywu/pengziyu/0108-4zy4-3/ligand/lig.frcmod"
loadamberprep "/home/lywu/pengziyu/0108-4zy4-3/ligand/lig.prep"
mol = loadpdb "/home/lywu/pengziyu/0108-4zy4-3/ligand/lig_4zy4-t28.pdb"
pro = loadpdb "/home/lywu/pengziyu/0108-4zy4-3/protein/4zy4_pred.pdb"


saveamberparm pro pro.prmtop pro.inpcrd
saveamberparm mol lig.prmtop lig.inpcrd
saveamberparm com native.prmtop native.inpcrd
savepdb com com-dry.pdb


charge com
solvatebox com OPCBOX 12
addionsrand com Na+ 15


saveAmberParm com complex.prmtop complex.inpcrd
savePdb com complex.pdb
quit
(Exiting LEaP: Errors = 0; Warnings = 14; Notes = 13.)

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
 #endif
 
  ; Include Position restraint file（分号不能省略）
 #ifdef  POSRES
 #include "posre2.itp
 #endif
 
  ; Include Position restraint file（分号不能省略）
 #ifdef  POSRES
 #include "posre3.itp
 #endif
 
 source ~/.gmx2022.5-remd.sh
 gmx_mpi genrestr -f gmx.gro -o posre1.itp
 vi posre1.itp | delete 4621
 cp posre1.itp posre2.itp
 sed -n '1,57p' posre1.itp > posre3.itp

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


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 &


gmx_mpi grompp -f ../mdp/nvt.mdp -c ../em/em.gro -r ../em/em.gro -p ../gmx.top -o nvt.tpr
nohup mpirun -np 100 gmx_mpi mdrun -v -deffnm nvt &


gmx_mpi grompp -f ../mdp/npt.mdp -c ../nvt/nvt.gro -r ../nvt/nvt.gro -p ../gmx.top -o npt.tpr
nohup gmx_mpi mdrun -v -deffnm npt &

gmx_mpi make_ndx -f gmx.gro -o index-system.ndx
>0
source ~/.gmx-2022.5-GPU.sh




md-200ns/1
export CUDA_VISIBLE_DEVICES=0
gmx_mpi grompp -f ../../mdp/md-200ns.mdp -c ../../npt/npt.gro -t ../../npt/npt.cpt -p ../../gmx.top -n ../../index.ndx -o md.tpr
nohup gmx_mpi mdrun -v -deffnm md &






md-200ns/2
export CUDA_VISIBLE_DEVICES=2
gmx_mpi grompp -f ../../mdp/md-200ns.mdp -c ../../npt/npt.gro -t ../../npt/npt.cpt -p ../../gmx.top -n ../../index.ndx -o md.tpr
nohup gmx_mpi mdrun -v -deffnm md &




md-200ns/3
export CUDA_VISIBLE_DEVICES=3
gmx_mpi grompp -f ../../mdp/md-200ns.mdp -c ../../npt/npt.gro -t ../../npt/npt.cpt -p ../../gmx.top -n ../../index.ndx -o md.tpr
nohup gmx_mpi mdrun -v -deffnm md &

md-200ns/4
export CUDA_VISIBLE_DEVICES=0
gmx_mpi grompp -f ../../mdp/md-200ns.mdp -c ../../npt/npt.gro -t ../../npt/npt.cpt -p ../../gmx.top -n ../../index-system.ndx -o md.tprnohup gmx_mpi mdrun -v -deffnm md &


md-200ns/5
export CUDA_VISIBLE_DEVICES=1
gmx_mpi grompp -f ../../mdp/md-200ns.mdp -c ../../npt/npt.gro -t ../../npt/npt.cpt -p ../../gmx.top -n ../../index-system.ndx -o md.tprnohup gmx_mpi mdrun -v -deffnm md &