[gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

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>> 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>>> 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> | (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

========================================