Albert,
You need a colon before 290 to designate it as residue 290 to be consistent
with AmberMask syntax. i.e. "-n :290" instead of "-n 290".
-Bill
On Tue, Apr 2, 2013 at 2:18 PM, Albert <mailmd2011.gmail.com> wrote:
> Hello :
>
> I am trying to run ante-MMPBSA with following command:
>
> ante-MMPBSA.py -p ../sys.prmtop -c ../npt4.trj -c
> complex_unsolvated.prmtop -r receptor.prmtop -l ligand.prmtop -s ':WAT'
> -n '290'
>
> but it failed with messages:
>
>
>
>
> Stripping :WAT (solvent) from original topology, output is
> complex_unsolvated.prmtop
> Done stripping solvent!
>
> Creating receptor topology file by stripping 290 from
> complex_unsolvated.prmtop
> Error: Creating receptor topology failed!
> Loaded Amber topology file complex_unsolvated.prmtop
>
> Reading input from STDIN...
> >
> MaskError: AmberMask: Bad syntax
>
> thank you very much
> best
> Albert
>
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Tue Apr 02 2013 - 12:00:03 PDT
