Dear David,
Yes, I want to keep some part of the system rigid. let's say, a group
of residues.
Sincerely,
On Thu, Feb 1, 2018 at 2:31 PM, David A Case <david.case.rutgers.edu> wrote:
> 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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--
Armin Hodaei
Department of Physics,
Faculty of Arts and Sciences
Koc University, Istanbul
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Received on Thu Feb 01 2018 - 05:00:02 PST
