[gmx-users] Re: multiple protein interaction

Justin A. Lemkul jalemkul at vt.edu
Thu Jul 28 14:48:44 CEST 2011

smriti Sebastian wrote:
> hi,
> According to the help frm gmx-users ,
> I did editconf with -center option twice.concatenated the coordinate 
> files using cat.
> Then i ran frm pdb2gmx till genbox..When I saw result pdb using pymol 
> there was only one protein inside the box.Why is it like that?When i 
> opened the gro file after pdb2gmx number of atoms were double than the 
> original one.
> wht would be the problem?please help
> These are the commands which i performed:
> pdb2gmx -f 1lyd.pdb -o lyzo
> editconf -f lyzo -bt cubic -d 1 -center 1 -o lyzo_edit.pdb
> editconf -f lyzo -bt cubic -d 1 -center 1 -o lyzo_edit1.pdb
> cat lyzo_edit.pdb lyzo_edit1.pdb > lyzozym.pdb
> pdb2gmx -f lyzozym.pdb -o lyzozy
> editconf -f  lyzozy -bt cubic -d 1 -center 1 -o lyzozy_edit -c
> genbox -cp lyzozy_edit -cs spc216 -o lyzozy_gen.pdb
> Thanks in advance

You're centering both proteins at (1,1,1) so they overlap.  The proper approach 
is to define a box that is of sufficient size and shape to accommodate both 
proteins (editconf -box) and place them at different locations and orientations 
within it (using editconf -translate/-center/-rotate as necessary).

> smriti
> On Tue, Jul 26, 2011 at 8:09 PM, <gmx-users-request at gromacs.org 
> <mailto:gmx-users-request at gromacs.org>> wrote:

Please do not reply to the entire digest.  It makes the archive hopelessly 



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


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