[gmx-users] hbonds(non covalent) contraint
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Fri Feb 13 23:20:02 CET 2004
First, define a custom group of atoms you wish to restrain using make_ndx:
make_ndx -f my_protein.gro -n index.ndx
For example, to define a group containing C-alpha atoms of residues
100-125, at the prompt you would type:
>r 100-125 & a CA
Next, use genpr to generate a position restraint itp file corresponding
to that custom group:
genpr -f my_protein.gro -n index.ndx -o my_res.itp
and select the desired group at the prompt.
Please, see the Manual or the online Reference for details.
Lakshmi Padmavathi wrote:
>Dear gromacs users,
> I have a protein which contains 12 helices. while doing simulation
>I would like to constrain or restraint the hbonds between the two turns of
>helix to constraint the alpha- helix structure.
>how can i do this? to write the distance restrints, i have to write hundres of
>atoms, is there any other was to maintain the helix structure trought the
>very thankful for your suggestions.
>thank you very much.
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