AMBER Archive (2006)

Subject: Re: AMBER: Problems using rst distance constraints in Amber 8

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 20 2006 - 14:12:20 CDT

On Wed, Sep 20, 2006, Whitney Allen wrote:

> I have run this code to constrain distances between atoms using Amber 7
> and the restraints work well (in this case I want to constraint the
> distance between two atoms in four separate cases) However, when I use
> this same code in Amber 8 no restraints are found in my output file. Has
> there been a change in the input format? How should I format the distance
> constraints?
>
> equilibrate the structure
> &cntrl
> imin=0, ntx=5,
> irest=1, ntxo=1,cut=15.0, tempi=300.0,
> ntpr=1000, ntwx=1000, ntwe=1000,
> nstlim=4000000,tautp=2, temp0=300.0,
> dt=0.001, nscm=100,
> igb=1,ntb=0, saltcon=0.5, gbsa=1,
> ntt=1, nsnb=20,offset=0.13, ntr=0,
> nmropt=1,
> &end
> &wt
> type='END'
> &end
> &rst iat=19,1938,
> ir6=0,
> r1=0.0, r2=0.5, r3=4.5, r4=9.0,
> rk2=0.2, rk3=0.2,
> &end

Starting with version 8, the restraints must be in the DISANG file, and cannot
be in the mdin file anymore. (See the second full paragraph on p. 119 of
the Amber 8 users' manual.)

Sorry that this tripped you up. We try not to make changes that cripple
existing input files, but in this case we felt we had to make an exception.
(It was a mistake to ever allow restraints in the mdin file in the first
place).

So, just create a file that has the distance restraints, and use the use the
"DISANG=filename" redirection command to point to it. This should work in
both Amber7 and Amber 8.

....good luck...dac

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