Atomistic simulation of Rab5a and amino acid chain

Atomistic simulation of Rab5a

Materials: GROMACS, CORI, PDB (www.rcsb.org)

• If stuck on steps below, follow steps from link:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/01_pdb2gmx.html

• download 1n6h.pdb which is found on https://www.rcsb.org/structure/1n6h
• cp 1n6h.pdb 1n6h_clean.pdb
• grep GNP 1n6h_clean.pdb > GNP.pdb

For example: “HETATM”

• grep -v "HETATM" 1n6h_clean.pdb > AA.pdb

Made AA.pdb that did not include “HETATM”

1n6h_clean.pdb was renamed 1n6h_dirty.pdb

removed 1n6h_clean.pdb

AA.pdb was renamed 1n6h_clean.pdb

removed AA.pdb

• gmx pdb2gmx -f 1n6h_clean.pdb -o 1n6h_processed.gro -water spc

Picked 9: GROMOS96 43a1 force field

• cp 1n6h_processed.gro complex.gro
• gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
• gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
• download em.mdp
• gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 1
• gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -np 1

Picked: Group 13 (SOL) has 23028 elements

Basically generated topol.top from this command

• download em_real.mdp

erased JZ4 in nano em_real.mdp

• gmx grompp -f em_real.mdp -c solv_ions.gro -p topol.top -o em.tpr -maxwarn 1
• gmx mdrun -v -deffnm em
• gmx make_ndx -f em.gro -o index.ndx

Picked 1 Protein

hit q

• download nvt.mdp

Removed JZ4 from nvt.mdp

• gmx grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr -r em.gro
• gmx mdrun -deffnm nvt
• download npt.mdp

removed JZ4 lines from npt.mdp

transferred the whole experiment file from terminal to cori

• ssh bsanchez@cori.nersc.gov
• module load gromacs (terminal needs to be reminded about gromacs)
• gmx_sp grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr -r em.gro
• salloc -N 1 -C haswell -q interactive -t 02:00:00 (request job)
• module load gromacs
• srun -n 16 mdrun_mpi_sp -deffnm nvt
• gmx_sp grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
• srun -n 16 mdrun_mpi_sp -deffnm npt
• download md.mdp

removed JZ4 lines

transferred it to cori by filezilla

• module load gromacs
• gmx_sp grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_1.tpr
• srun -n 16 mdrun_mpi_sp -deffnm md_0_1
• gmx_sp trjconv -f md_0_1.xtc -s md_0_1.tpr -o md_centered.xtc -pbc mol -center

Pick 1 Protein

Pick 0 System

• vmd npt.gro md_centered.xtc

• Atomistic simulation of amino acid chain is the same as these steps.