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-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>> wrote:
Please do not reply to the entire digest. It makes the archive hopelessly
confusing.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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