[gmx-users] Re: Inflategro for Coarse Grained

[sunny mishra]

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

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> 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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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