mktonycho / membraneprotein Goto Github PK

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

Step 1
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gmx_mpi pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water spc
	GROMOS96 53A6 parameter set. Choose "None" for the termini; 

Step 2
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	create directory: gromos53a6_lipid.ff/

Step 3
======
gmx_mpi editconf -f dppc128.pdb -o dppc128.gro 

gmx_mpi grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr


gmx_mpi trjconv -s em.tpr -f dppc128.gro -o dppc128_whole.gro -pbc mol -ur compact
	Select a group: 0

gmx_mpi editconf -f KALP-15_processed.gro -o KALP_newbox.gro -c -box 6.41840 6.44350 6.59650

   (for other systems...) gmx_mpi editconf -f protein.gro -o protein_newbox.gro -box  6.41840 6.44350 6.59650 -center 3.20920  3.22175  3.29825 

cat KALP_newbox.gro dppc128_whole.gro > system.gro


gmx_mpi genrestr -f KALP_newbox.gro -o strong_posre.itp -fc 100000 100000 100000