you can apply a distance restraint between the centers of mass of two groups.
It is described in the Amber9 manual starting at page 178. You will want to
use the igr1() and igr2() groups described starting at page 181. For lots of
atoms it can be a pain to produce the input files, you might want to
use a script
or something similar to make them. It's also a good idea to have experience with
regular distance retraints first, there are examples in the amber distribution
and they have been discussed extensively on the email list in the past, so you
might check the archives.
On 8/15/07, Sudha Mani Karra <karra.md.gmail.com> wrote:
> Dear Amber users,
> I would like to apply simple harmonic distance restraints
> between center of mass of two molecules. I
> could understand from the previous threads that the distance restraint can
> be applied between two atoms.Could anyone explain how this can be done?
> I appreciate for your inputs.
> Thanks,
> Sudha.
>
>
>
>
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Received on Sun Aug 19 2007 - 06:07:08 PDT
