[gmx-users] part of protein in protein complex out of the box (system preparation) -reg

venkatesh s svenkateshbioinformatics at gmail.com
Sat Nov 3 15:54:42 CET 2012

Respected Gromacs Peoples,
                  My task is protein protein interaction ( 3 protein in
total,399 residues) i chose opls ff and tip3p water model after salvation
step i took the pdb file,part of the protein out side the box (octahedron).

following commands used

pdb2gmx -f final.pdb -o processed.gro -ignh -chainsep ter

editconf -f processed.gro -o plg_newbox.gro -c -d 1.0 -bt dodecahedron

genbox -cp plg_newbox.gro -cs spc216.gro -o plyg_solv.gro -p topol.top

editconf -f plyg_solv.gro -o plyg_box_check_dodecahedron_tip3p.pdb

Kindly Provide prompt answer
Thank you

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