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- #su Chimera istraukti SAM pdb (SAM.pdb).
- #tik chain A ir SAM atskiruose failuose ir dockprep
- #tada su Chimera atgal i pdb fix
- export PATH=$PATH:/home/vytautas/bin/amber16/bin/ && export AMBERHOME=/home/vytautas/bin/amber16
- #Chimeros amber:
- #export PATH=$PATH:/home/vytautas/.local/UCSF-Chimera64-1.14/bin/amber18/bin/ && export AMBERHOME=/home/vytautas/.local/UCSF-Chimera64-1.14/bin/amber18
- acpype -i SAM_fix.pdb -n 1
- Pasirinktas:
- 6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
- #pymol states buvo trys imta 1, nes tinka seka.
- gmx pdb2gmx -f 6W4H_A_fix.pdb -o 6W4H_processed.gro -water spce -ignh
- #SAM_fix.acpype/SAM_fix_GMX.gro
- #i 6W4H_processed.gro gala ir virsuj nr. prideti atomu sk.
- #i topol.top pradzioj:
- #include "SAM_fix.acpype/SAM_fix_GMX.itp"
- #O gale:
- #SAM_fix 1
- #box:
- gmx editconf -f 6W4H_processed.gro -o 6W4H_newbox.gro -c -d 1.0 -bt cubic
- #vanduo:
- gmx solvate -cp 6W4H_newbox.gro -cs spc216.gro -o 6W4H_solv.gro -p topol.top
- #jonai:
- #wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/ions.mdp :(
- #cp ~/MD_Cx43_lycopene_DOCK_2/*.mdp .
- gmx grompp -f ions.mdp -c 6W4H_solv.gro -p topol.top -o ions.tpr
- gmx genion -s ions.tpr -o 6W4H_solv_ions.gro -p topol.top -neutral
- #minimizacija:
- #wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/minim.mdp
- gmx grompp -f minim.mdp -c 6W4H_solv_ions.gro -p topol.top -o em.tpr
- gmx mdrun -v -deffnm em
- #Equilibration
- #wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/nvt.mdp
- gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr
- gmx mdrun -deffnm nvt
- #Equilibration 2
- #wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/npt.mdp
- gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
- gmx mdrun -deffnm npt
- #MD run:
- #wget http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/Files/md.mdp
- gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr
- gmx mdrun -deffnm md_0_1
- #testi nuo checkpointo:
- gmx mdrun -v -deffnm md_0_1 -cpi md_0_1.cpt
- #rez i pdb:
- gmx trjconv -f md_0_1.trr -s md_0_1.gro -skip 10 -o md_0_1.pdb
- #kisenes ner :\
- #tiksliau paziureti:
- #nstxout = 50 ; save coordinates
- gmx trjconv -f em.trr -s em.gro -o em.pdb
- PyMOL>cealign 6w4h__state01, em
- PyMOL>zoom hexanol_kisenej
- gmx trjconv -f md_0_1.trr -fit rot+trans -s md_0_1.gro -skip 10 -o md_0_1.pdb
- #atstumai tarp CIS 92 sieros ir CIS 264 sieros grafiku:
- ; Paskaiciuot atstumus nuo laiko:
- ;
- ; Use "gmx distance -n index.ndx -f md_0_1.trr -s md_0_1.tpr -oav -oall"
- ; with index file write in this way:
- ;
- [SG_92 - SG_1203]
- 1477 19736
- #paskui:
- xmgrace dist.xvg
- #energija:
- gmx energy -f md_0_1.edr -o md_ener.xvg
- #rms:
- gmx rms -s md_0_1.tpr -f md_0_1.xtc
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