[gmx-users] hbonds(non covalent) contraint

Martina Bertsch, PhD mbe404 at lulu.it.northwestern.edu
Fri Feb 13 23:20:02 CET 2004

Dear Lakshmi,

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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>gmx-users at gromacs.org
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