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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Received on Sat Sep 15 2012 - 05:00:03 PDT
