sunny mishra wrote:
Alright. I have done this....I have made another lipid_newbox.gro file
and wrote same box vectors as of lipid.gro file
For LIPID :
editconf -f lipid.gro -o lipid_newbox.gro -c -box 13.29820 13.29820 6.59160
For Protein :
editconf -f protein.gro -o protein_newbox.gro -c -box 13.29820 13.29820
6.59160
Then cat the system and made system.gro file and did inflategro of the
system.gro file. Do you think this is the correct way and now when I
visualize this in VMD the protein is shifted little upwards but it is at
the center of the lipid.
Well, did you get what you expected when you ran InflateGRO? The protein and
lipid should have the same center; that's what the editconf commands did, as
I've told you. If you need the protein to be placed differently, you must
specify a different center (providing the coordinates to editconf -center).
-Justin
Sunny
On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
sunny mishra wrote:
No. But in order to do that with lipid.gro what co-ordinates
should I have to take?
I think you need to differentiate between "coordinates" and "box
vectors." You should center the molecule in the box (defined by the
vectors in the last line of the .gro file). I assumed you were
specifying these box vectors with -box.
So, for both the protein and the lipid coordinate files, you need to use
editconf -c -box (x, y, z from .gro file)
-Justin
On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul
<[email protected] <mailto:[email protected]>
<mailto:[email protected] <mailto:[email protected]>>> wrote:
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]>
<mailto:[email protected] <mailto:[email protected]>>
<mailto:[email protected] <mailto:[email protected]>
<mailto:[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> <http://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 <http://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 <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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