I tried the modification you suggested, but still no joy. Still getting the
same error. It seems to indicate that there is something wrong with the
distance restraint file. However, I checked and atom numbers, etc seem all
correct. What do you think?
On Tue, Sep 23, 2014 at 4:30 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Tue, 2014-09-23 at 14:39 +0100, George Green wrote:
> > I'm trying to run a simulation that uses a single harmonic restraint
> > simultaneously with a distance restraint. The pmemd simulation crashes
> with
> > the following error:
> >
> > ################
> > 5. REFERENCE ATOM COORDINATES
> >
> > default_name
> >
> > ----- READING GROUP 1; TITLE:
> > LISTOUT=POUT
> >
> >
> > rfree: Error decoding variable 1 3 from:
> > DISANG=restraint_list.dist
> > #################
> >
> >
> > Using just NTR or nmropt on their own seems to work with no problems, so
> I
> > think this is a syntax issue. I don't have much experience with
> restraints,
> > so I am having difficulty seeing where things are going wrong here.
> >
> > My input files are:
> > ##########################
> > &cntrl
> > nstlim=20000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=50000, ntwx=100,
> > temp0=300.0, ntt=1, tautp=2.0, ioutfm=1, ntxo=2, ig=-1,
> >
> > ntb=2, ntp=1, ntc=2, ntf=2,
> >
> > nrespa=1, NTR=1, nmropt=1,
> > &end
> > &wt type='END'
> > &end
> > LISTOUT=POUT
> > DISANG=restraint_list.dist
> > Group input for restrained atoms
> > 30
> > RES 1
>
> This needs to be a residue range. For example:
>
> RES 1 100
>
> RES 1 50
>
> If you just want residue 1:
>
> RES 1 1
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue Sep 23 2014 - 12:30:02 PDT
