AMBER Archive (2009)

Subject: RE: [AMBER] generalized distance restraint

From: Rausch, Felix (frausch_at_ipb-halle.de)
Date: Mon Mar 09 2009 - 11:15:11 CDT

Thank you for your fast reply.
Im sorry that my first mail wasnt accurate enough.

Until now, i started all my Steered MDs with Amber10 for free energy
calculations with restraints like this:

&rst iat=8879, 8458, r2=2.625, rk2=50, r2a=1.0,
/

With the jar option set to 1 for SMD, the missing parameters will be set
automatically. In the output, the restraint looks like the following:

jar option running
******
 H82 ( 8879)-OH ( 8458) NSTEP1= 0
NSTEP2=500000
R1 = -97.375 R2 = 2.625 R3 = 2.625 R4 = 102.625 RK2 = 50.000 RK3 =
50.000
R1A= -99.000 R2A= 1.000 R3A= 1.000 R4A= 101.000 RK2A= 50.000 RK3A=
50.000
 Rcurr: 2.626 Rcurr-(R2+R3)/2: 0.001 MIN(Rcurr-R2,Rcurr-R3): 0.001
                       Number of restraints read = 1

Now i want to start a SMD with two different restraints running in parallel
over the time of a MD (described in the manual p. 168f ?). Goal is the same
as doing a normal SMD, a free energy calculation. So i thought just adding
another &rst line to the REST-file would work, but i only get an error
message or only the first restraint is recognized.

Input .REST:

&rst iat=4676, 1583 r2=3.792, rk2=50, r2a=1.00,
&rst iat=4657, 4671 r2=3.897, rk2=50, r2a=1.5,
/

Output:

 jar option running
******
 H5 ( 4676)-OD1 ( 1583) NSTEP1= 0
NSTEP2=250000
R1 = -96.208 R2 = 3.792 R3 = 3.792 R4 = 103.792 RK2 = 50.000 RK3 =
50.000
R1A= -99.000 R2A= 1.000 R3A= 1.000 R4A= 101.000 RK2A= 50.000 RK3A=
50.000
 Rcurr: 3.792 Rcurr-(R2+R3)/2: 0.000 MIN(Rcurr-R2,Rcurr-R3): 0.000
                       Number of restraints read = 1

                    Done reading weight changes/NMR restraints

I hope that someone tried a similar task or has an example of such
restraint(s) so i can get an idea of how to fit my values to the required
format given in the manual.

Thanks,
Felix Rausch

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Carlos Simmerling
Sent: Mon 3/9/2009 4:13 PM
To: AMBER Mailing List
Cc:
Subject: Re: [AMBER] generalized distance restraint
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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> AMBER_at_ambermd.org
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>

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