[gmx-users] Re: Inflategro for Coarse Grained
Justin A. Lemkul
jalemkul at vt.edu
Thu Oct 29 22:26:07 CET 2009
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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> 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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