On Thu, Feb 01, 2018, ARMIN HODAEI wrote:
>
> I am trying to restrain the distance of a group of residues on a
> protein. I know that I have to use "sander" and impose NMR restraints(based
> on AMBER manual). But as far as I understand, I have to do it for every
> atom, and there are lots of atoms in these target residues. So is there a
> better way to just use the residue numbers, and fix the initial distances,
> in a way that they would not change during the MD simulations?
It's unclear (to me) what you mean by "restrain the distance of a group
of residues...": what distance(s) do you wish to restrain?
Are you (perhaps) trying to keep some part of the system rigid?
NMR distance restraints are intrinsically atom or center-of-mass based
restraints. Would it help to restrain the distances between the centers of
mass of various residues?
Otherwise, if you have lots of distances, you may need to write a script
to prepare the restraint input.
....good luck....dac
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Received on Thu Feb 01 2018 - 05:00:02 PST
