AMBER Archive (2009)

Subject: Re: [AMBER] generalized distance restraint

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Mar 09 2009 - 10:13:50 CDT

does the restraint you sent actually work? I would think maybe no, due
to missing commas and not defining some of the variables like r3 etc.
maybe the defaults are ok, but read the sander output carefully to
make sure it is exactly what you want.
regarding multiple restraints, it is certainly possible to set
multiple restraints and have them all changing at the same time.
whether you need "generalized" restraints depends on what you are
trying to do, which you haven't really said. is this for a free energy
calculation? do you need a single restraint that changes multiple
distances? try to clarify and more people might be able to help out.

On Mon, Mar 9, 2009 at 9:48 AM, Rausch, Felix <frausch_at_ipb-halle.de> wrote:
>
> Dear amber users,
>
> I already started some Steered MD caclulations. Since I cant get the
> makeDIST_RST program work properly I generated the REST-files by hand. They
> look like the following:
>
>  &rst iat=4676, 1583 r2=3.792, rk2=50, r2a=1.00,
>  /
>
> Now i want to set up a calculation with 2 constraints at the same time,
> something like "Decrease distance between atoms A and B while increasing
> distance between atoms C and D". I read in the manual that this is possible
> by the use of a generalized distance restraint constraint.
>
> Is there anybody who already set up such a job who can maybe help me
> generating a REST-file for this task? Despite reading the manual, im not sure
> how to modify my REST-file to set the right parameters.
>
> Thanks in advance,
> Felix Rausch
>
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