[gmx-users] hbond calculation in peptide-membrane simulation

[manindersingh rajawat]

Dear gromacs users,
I performed 200ns MD simulations (gromacs 5.0.7) of peptide and mixed lipid
bilayer (POPS:POPC). Initially placed 6 copies of the peptide parallely
over the surface of the lipid bilayer (128 lipids). I want to calculate
hydrogen bond occupancy using hbond tool between peptide and lipids over
the simulation time. How to make index file for it. What atoms I should put
in index file.
Please advise with appropriate commands.
Thanks and regards,
Maninder


-- 
Maninder Singh
Research Fellow,
LSN-104, Computational Biology and Bioinformatics Unit,
Molecular and Structural Biology Division,
CSIR-Central Drug Research Institute,
Sector-10, Janakipuram Extension,
Sitapur road,
Lucknow
India-226031
M: +919129206276
Email: rajawat.manindersingh at gmail.com