strip_mask is not a command line option for MMPBSA.py. If you want to
specify strip_mask then you should include it in your mmpbsa.in file.
However, I doubt you will need to specify it since MMPBSA.py should remove
all ions and water molecules from the original trajectory file by default.
-Bill
On Mon, Sep 5, 2011 at 2:56 PM, kirtana S <skirtana4.gmail.com> wrote:
> I am using MMPBSA.py to calculate the energy for only complex.While
> specifying the input files I am doing some mistake please suggest
>
> Error: mdcrd file (strip_mask) does not exist!
> Error: mdcrd file (:WAT) does not exist!
> kls_home/amber11/bin/MMPBSA -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp solv.prmtop -cp vac.prmtop -y md.x
> strip_mask :WAT
>
> md.x is my trajectory file (with WAT)
> solv.prmtop is the solvated topology file of my complex
> and vac.prmtop is the vacuum topology file of my complex
>
> Your suggestions are highly appreciated
>
> Thanks
> Kirtana
>
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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Sep 05 2011 - 14:00:03 PDT
