It sounds like you primarily want secondary structure restraints, which
might also naturally enforce (some) tertiary structures. This is used a lot
in low resolution structure refinement.
There's a VMD plugin that will generate these in NAMD format, but it
shouldn't be too hard to convert that to nmropt format using a script.
Ultimately the idea is to enforce ideal hydrogen bond distances in helices
and sheets.
Atom based distance restraints also have the advantage of being very
computationally efficient compared to exotic collective variables or
constraints.
HTH,
Brian
On Mon, Dec 16, 2019, 2:14 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> It’s been a while since I needed to restrain anything. However, there is
> one option to “freeze” things and there are other options to “restrain”
> tings. If you put a restraint on some movement there were also the option
> to specify the energy associated with the restraint. This way, you should
> be able to put a restraint on the things you need and set the associate
> energy at a level that still allows movement.
>
> Best regards
> // Gustaf
>
>
>
> > On 14 Dec 2019, at 05:59, Liao <liaojunzhuo.aliyun.com> wrote:
> >
> > Dear fellows,
> >
> > I’m trying to run MD with 2 proteins and a ligand. I want to make the
> protein as rigid as I can (still capable of translational and rotational
> movement). As far as I understand, adding atom restraints freezes each
> atom, and that doesn’t allow movement anymore. How could the above problem
> be solved?
> >
> > Thanks.
> >
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Received on Mon Dec 16 2019 - 07:30:02 PST
