section 29.1
On Fri, Apr 5, 2024 at 1:37 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Thanks Carlos
> Could you point me to the documentation in Amber22 manual?
>
> Thanks
> Debarati
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Thursday, April 4, 2024 4:59 PM
> *To:* Debarati DasGupta <debarati_dasgupta.hotmail.com>; AMBER Mailing
> List <amber.ambermd.org>
> *Subject:* Re: [AMBER] restraining a possible interaction between solute
> and ligand
>
> Why not use a distance restraint on that atom pair? Using nmropt.
>
> On Thu, Apr 4, 2024, 7:24 PM Debarati DasGupta via AMBER <
> amber.ambermd.org> wrote:
>
> Hello everyone
>
> I am trying to find some documentation to help me set up a distance based
> restraint between an NH2 group in my receptor and a C=O group in my ligand.
>
> I basically wanted to keep the "potential Hbonding" interaction weakly
> restrained during 10-20ns of equilibration.
> Do you think if I used ntr=1 and restraintmask on the LIG alone I would be
> able to in a way achieve the same task? My receptor backbone is restrained
> during first 2 cycles of equilibration
>
>
> Thanks
> Debarati
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Received on Fri Apr 05 2024 - 11:00:02 PDT
