[gmx-users] Re: Inflategro for Coarse Grained

[Justin A. Lemkul]

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>> 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

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