[gmx-users] Re: Inflategro for Coarse Grained
sunny mishra
mishra.sunny at gmail.com
Thu Oct 29 22:23:23 CET 2009
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.
Sunny
On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul <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>> 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
>>
>> ========================================
>> _______________________________________________
>> gmx-users mailing list gmx-users at gromacs.org
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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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
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