[gmx-users] Re: Inflategro for Coarse Grained

Justin A. Lemkul jalemkul at vt.edu
Thu Oct 29 22:26:07 CET 2009



sunny mishra wrote:
> 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.
> 

Well, did you get what you expected when you ran InflateGRO?  The protein and 
lipid should have the same center; that's what the editconf commands did, as 
I've told you.  If you need the protein to be placed differently, you must 
specify a different center (providing the coordinates to editconf -center).

-Justin

> Sunny
>        
> 
> On Thu, Oct 29, 2009 at 4:59 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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>
>         <mailto: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>>
>                <mailto: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>
>         <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> <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

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



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