sunny mishra wrote:
okk...here are the commands which I am givng...
editconf -f 1SU4_cleancg_trans.gro -o 1SU4_newbox.gro -c -box 13.29820
13.29820 6.59160
I get the 1SU4_newbox.gro which has co-ordinates 13.29820 13.29820 6.59160
Have you done the same with lipid.gro? If the protein and the lipid are in
different coordinate systems (i.e., lipid.gro centered at the origin and protein
centered within the box, which has its corner placed at the origin) then you
will have a problem.
-Justin
cat 1SU4_newbox.gro lipid.gro > system..gro
Now here system.gro also has co-ordinates 13.29820 13.29820 6.59160
now inflategro:
inflategro system.gro 4 DSPC 14 -o inflated_bilayer.gro 5
Now when i visualize my output file in VMD then protein and lipid are
seperated and even after i scale it to .95 they dnt meet....they are
still apart, I was hoping that lipid will be scaled and protein shud
have remained in the center of the lipid but that doesn't happen. I hope
you got my question
On Thu, Oct 29, 2009 at 4:25 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
sunny mishra wrote:
Yes I did the same and when I see my system.gro file it gives me
the dimensions of the protein box half of the lipid bilayer box
so that means it should now be set in the center of the lipid
bilayer. But after
I don't understand what you mean.
that when I run the inflategro script and see my output file the
protein and lipid are separated and I dnt know why?
Can you post the actual commands you're using?
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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