[gmx-users] Re: Inflategro for Coarse Grained

[sunny mishra]

No. But in order to do that with lipid.gro what co-ordinates should I have
to take?

On Thu, Oct 29, 2009 at 4:40 PM, Justin A. Lemkul <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>> 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
>
> ========================================
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