[gmx-users] couple of questions about H-bonds and constraints

[Anton Feenstra]

Dastmalchi wrote:

> Hi there,
> 
> 1) I want to keep the secondary structure conformations in different
> parts of my protein structure fixed, say for example, residues 20-40,
[...]

You'd want to add explicit interactions to these H-bonds. Simplest, 
perhaps, would be to add distance restraints ('disres') as are used in NMR 
structure refinement. In essence, they are harmonic potentials with a few 
additional (and optional) features. The manual explains the syntax of these 
sections in your topology (.top) file, but basically, like bonds, they will 
be a list of atom pairs and corresponding parameters. I'm not sure if 
restraining the donor-acceptor, or the hydrogen-acceptor distance would 
work best.

-- 
Groetjes,

Anton

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|  _   _  ___,| K. Anton Feenstra                                     |
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