[gmx-users] Calculate a single hydrogen bond energy in the polypeptide molecule

[Anton Feenstra]

Sekwan Oh wrote:

> Dear gmx-users,
> 
> I'm wondering if we can obtain hydrogen bond energy (e.g. N-H ----- O=C) 
> in the polypeptide molecule (which is defined as 1 group of residues e.g 
> LYSH).
> I think I can get the bonded and nonbonded energy of the 1 residue of 
> the polypeptide (by using g_energy and setting up 'energygrp' command in 
> .mdp file)
> , however I haven't found out a way to get the energy between atoms 
> which belong to same group of residues.

You can, if you make your own .mdp file in which you define two groups,
one corresponding to your N-H of interest, and the other to your O=C.
Assuming you name these groups, e.g., 'N-H' and 'O=C', your .ndx file
could look like:

[Protein]
1 2 3 ...
[SOL]
4513 4514 ...
[N-H]
45 46
[O=C]
61 62

And your .mdp file will contain:

energy_grps = N-H O=C

Using g_energy (after the simulation or the rerun), you can find the
N-H-O=C groups to analyze.

-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
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