[gmx-users] Problem with Inflategro!!!
jalemkul at vt.edu
Wed Jul 18 13:56:20 CEST 2012
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
> 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
3. Concatenate the protein and bilayer coordinate files and adjust number of
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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