Dear all,
I performed 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.
If you can import the trajectory frames into the VMD, the hydrogen bond analysis of VMD can be helpful to calculate the occupancy of the hydrogen bonds.
You can make two index group one having peptide and other having lipid. gmx hbond takes OH, NH groups as donor and OH and O and N are acceptor by default. gmx hbond -h command you see rest of details.
Thank you Pritam, Rahim and Tasneem for your suggestions.
I have grouped POPC and POPS lipids in index file and run gromacs hbond tool by following commands.
gmx make_ndx -f md_200ns.tpr -o hbond.ndx
> 2|3
28 : POPS_POPC : 16977 atoms
gmx hbond -f md.xtc -s md.tpr -n hbond.ndx -num hbond1.xvg -hx hbond2.xvg -hbn hbond3.xvg -hbm hbond4.xvg
Calculating hydrogen bonds between Protein (1374 atoms) and POPS_POPC (16977 atoms)
Found 127 donors and 1382 acceptors
error: Your computational box has shrunk too much.
gmx can not handle this situation, sorry.
But stuck with the box error. How do I resolve this issue?
In VMD output file shows the existence of 162 hydrogen bonds between 'protein' and 'lipid'. But only between protein and POPC lipid molecules. Not with a POPS. Is it possible?
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