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

Justin Lemkul jalemkul at vt.edu
Sat Nov 3 15:56:30 CET 2012

On 11/3/12 10:54 AM, venkatesh s wrote:
> 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).

There is no such thing as "outside" a periodic unit cell.



> 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


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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