does sander tell you in the output file that it read the restraint input?
it should have a section telling how many restraints it read, etc.
you might be better off changing the r1/r2/r3/r4 values using r1a/r2a/r3a/r4a
rather than changing the REST weight. that way it will not have high forces and
you can slowly shift it 180 deg.
On 8/14/07, Tom Pochapsky <pochapsk.brandeis.edu> wrote:
> I am trying to force a cis -> trans isomerization of a peptide bond
> during a standard solvated MD simulation using Amber 8. I have
> included a standard torsion restraint file to be applied gradually
> during the simulation, but cannot detect any change; furthermore, no
> torsional energies are reported in md.out , its as if the restraint is
> not being applied. Any suggestions?
>
> Thanks,
> Tom Pochapsky
> Here is the md control file and the restraint file.
> md.in
> > &cntrl
> > imin=0, irest=1, ntx=7, tempi=0.0,
> > ntt=3, temp0=300.0, tautp=1.0, nmropt=1,
> > ntp=1, taup=2.0, nrespa=1,
> > ntb=2, ntc=2, ntf=2,
> > nstlim=60000, dt=0.001,
> > ntwe=1000, ntwx=1000, ntpr=1000,
> > gamma_ln=10,
> > /
> > #
> > #weight change for cis ->trans isomerization
> > #
> >
> > &wt type='REST',
> > istep1=0,istep2=60000,value1=1.0,
> > value2=10.0,
> > /
> >
> >
> >
> > &wt type='END' /
> > LISTOUT=POUT
> >
> > DISANG=RST
> RST
> > 84 PRO OMEGA: (83 CYS CA)-(83 CYS C)-(84 PRO N)-(84 PRO CA) -530.0 -180.0
> > &rst iat = 1321, 1336, 1338, 1348,
> > r1 = -531.0, r2 = -530.0, r3 = -180.0, r4 = -179.0,
> > rk2 = 100.0, rk3 = 100.0, &end
>
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Received on Wed Aug 15 2007 - 06:07:56 PDT
