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
--
========================================
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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