On 5/21/16 8:54 AM, Antara mazumdar wrote:
Dear Gromacs users,
I have a membrane protein simulation performed with gromacs 4.6. I have
calculated the minimum distance of protein residues from upper leaflet of
the lipid bilayer. I also have the time wise atom pair contacts as an
output.
The following command i used :
g_mindist -f SYSTEM_FIT_SIM4_DT100.xtc -s MD_4_NOWATER.tpr -n ../index.ndx
-d 0.7 -o atompair -on numcontact -od mindist.xvg
The atom pair out output i got was as follow :
.00e+00 2412281928
1.00e+02 1630266151
2.00e+02 1630266151
3.00e+02 2410284225
4.00e+02 2412284225
5.00e+02 2412284225
6.00e+02 2410284225
7.00e+02 2410284225
8.00e+02 2410284225
9.00e+02 2410284225
1.00e+03 2405284225
1.10e+03 2411281928
1.20e+03 2412284225
1.30e+03 2332285163
1.40e+03 2411284225
1.50e+03 2410284225
1.60e+03 1555264261
1.70e+03 1555264261
1.80e+03 1555264261
1.90e+03 1554266958
2.00e+03 2389266958
2.10e+03 2411285163
2.20e+03 2412285163
2.30e+03 2412285163
2.40e+03 2410285163
2.50e+03 2410285163
2.60e+03 2412285163
I now need to find out time wise percentage of protein covering the
membrane. I want to know for instance, at time t=0ns, what is the protein
coverage % and similarly for the entire trajectory i want to calculate this.
Kindly suggest something!!
The solution was already suggested to you - calculated the buried surface area.
You can express that as a fraction of the protein's surface area.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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