Yes I went through and changed in now my mmpbsa.in . Now this works .
Thank you , I appreciate your help
On Mon, Sep 5, 2011 at 4:32 PM, Bill Miller III <brmilleriii.gmail.com> wrote:
> 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 - 14:00:07 PDT
