[gmx-users] Problem with Inflategro!!!

[Justin Lemkul]

On 7/18/12 7:48 AM, Manikam Sadasivam Saravanan wrote:
> my command to inflate was - perl inflategro.pl protein_popc.gro 4 POPC
> 14 system_inflated.gro 5 area.dat
>
> my gro file looks like,
>
> membrane protein in POPC 121-310KWITNOIONS
> 59522
>      1SER      N    1  -2.092  -1.832  -1.359
>      1SER    HT1    2  -2.149  -1.861  -1.436
>      1SER    HT2    3  -2.150  -1.809  -1.281
>      1SER     CA    4  -2.002  -1.942  -1.322
>       ...............
>     91ILE    OT1 1527   0.033   1.945  -1.049
>     91ILE    OT2 1528   0.057   1.922  -1.267
> continued by popc and sol
>      1POPC     N    1   2.963  -2.658   2.064
>      1POPC   C12    2   3.003  -2.713   2.196
>      1POPC   C13    3   2.954  -2.509   2.062
>       .........
>   8764SOL     OW57992   3.731   3.721  -2.405
>   8764SOL    HW157993   3.749   3.653  -2.341
>   8764SOL    HW257994   3.723   3.802  -2.353
>     11.13710  11.41790   7.60370
>
> when I inflate with box vectors value 11.13710  11.41790   7.60370, my
> protein is out of inflated lipid boundary.  if i change my value to

So these box vectors are the inflated ones, or the original?  Not that it 
matters much, I'm just confused.

> 1.39213   1.42723   0.00000 (dividing above value by half and half),

You're doing more than dividing by half, and a zero length for the z-dimension 
is nonsensical.  Do not manipulate the box vectors yourself.

> now my protein is at the center of inflated popc. but the area per
> lipid even after inflation is still only 0.148 nm2.
>

The small area per lipid is a consequence of the massive reduction in the box 
size that your manual vectors impose.

> should i use editconf with the whole .gro file containing protein,
> popc  or i have to separate my protein only as a new.gro file and
> perform editconf and then cat?
>

When I build these systems, I do the following:

1. Note the box vectors in the bilayer coordinate file (don't modify them)
2. Position protein in a box with those same vectors and (if necessary) 
translate its coordinates using editconf -center or editconf -translate/-rotate 
as needed.
3. Concatenate the protein and bilayer coordinate files and adjust number of 
atoms accordingly.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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