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 - 09:00:03 PDT
