Hi Jason,
yes.. i just realized it after submitting it here.. Thanks a lot though
Have nice day :)
On Sat, Sep 15, 2012 at 5:16 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>
> On Sep 15, 2012, at 6:14 AM, Jitesh Doshi <dosjitesh.gmail.com> wrote:
>
> > Hi all,
> > I am getting an error while running minimization of my protein ligand
> > system.
> >
> > I used ambertools 12 for preparing files and running sander on amber 9
> >
> > i get following error in minout file:
> >
> >
> > -------------------------------------------------------
> > Amber 9 SANDER 2006
> > -------------------------------------------------------
> >
> > | Run on 09/15/2012 at 14:06:32
> > [-O]verwriting output
> >
> > File Assignments:
> > | MDIN: complex-min.in
> >
> > | MDOUT: complex-min.out
> >
> > |INPCRD: complex-water.crd
> >
> > | PARM: complex-water.top
> >
> > |RESTRT: complex-min.rst
> >
> > | REFC: complex-water.crd
> >
> > | MDVEL: mdvel
> >
> > | MDEN: mden
> >
> > | MDCRD: mdcrd
> >
> > |MDINFO: mdinfo
> >
> > |INPDIP: inpdip
> >
> > |RSTDIP: rstdip
> >
> >
> >
> > Here is the input file:
> >
> > Initial minimisation of p38 MAPK anisomycin complex
> >
> > &cntrl
> >
> > imin=1, maxcyc=2500, ncyc=1000,
> >
> > ntpr=5,ntr=1,restraint_wt=10,
>
> You are missing a restraintmask variable to select the atoms you want to
> restrain.
>
> Sander was looking for GROUP style inputs at the end I the input file
> (unit 5), hence your error message.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
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>
--
Jitesh V. Doshi
Research Associate,
Bioinformatics Centre,
University of Pune.
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Received on Sat Sep 15 2012 - 05:30:03 PDT
