[gmx-users] InflateGRO and pentamer protein simulation

[Justin A. Lemkul]

xi zhao wrote:
> 
> 
> Dear sir :
> I want to a pentamer membrane protein, when I used InflateGRO.pl with 
> /DOUGHNUT Mode, the results were wrong, please help me! /

If you want any useful help, you'll have to do a whole lot better than simply 
saying "the results were wrong."  No one on this list will have any idea what 
you mean.  If you believe there is some error in the script itself, you're 
better off contacting its author.

-Justin

> 4 
> <http://cn.webmessenger.yahoo.com/index.php?t=1&to=eWlkPXpoYW94aWl0YzIwMDI-&sig=703fa929658518b2720b087c59cd85f2dabf8844>show 
> " [user at localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 
> 14 kk_inflated.gro 5 area.dat doughnut protein_subunits
> Doughnut mode activated. Protein coordinates will be translated by 
> subunit ....
> Reading.....
> Reading chain identifiers....
> Subunit 1:  atom 1 to  atom 3238
> Subunit 2:  atom 3239 to  atom 6476
> Subunit 3:  atom 6477 to  atom 9714
> Subunit 4:  atom 9715 to  atom 12952
> Subunit 5:  atom 12953 to  atom 16190
> There are 5 protein subunits....
> Scaling lipids....
> There are 512 lipids...
> with 65 atoms per lipid..
> Determining upper and lower leaflet...
> 256 lipids in the upper...
> 256 lipids in the lower leaflet
> Checking for overlap....
> ...this might actually take a while...
> .......
> Argument "N4" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C5" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C6" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "O7" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "P8" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "O9" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "A1" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "A2" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C1" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C2" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C3" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "N4" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C5" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "C6" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "O7" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "P8" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "O9" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "A1" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Argument "A2" isn't numeric in printf at inflategro.txt line 708, 
> <CHAINS> line 5.
> Calculating Area per lipid...
> Protein X-min/max: 23    105
> Protein Y-min/max: 18    100
> X-range: 82 A    Y-range: 82 A
> Building 82 X 82 2D grid on protein coordinates...
> Calculating area occupied by protein..
> full TMD..
> upper TMD....
> lower TMD....
> Area per protein: 49 nm^2
> Area per lipid: 9.83158146861789 nm^2
> Area per protein, upper half: 38.75 nm^2
> Area per lipid, upper leaflet : 9.79362516645161 nm^2
> Area per protein, lower half: 45.75 nm^2
> Area per lipid, lower leaflet : 9.92548787409836 nm^2
> Writing Area per lipid...
> Done!
> 
> 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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