Dear Dr. Jason,
Thank you for your rapid reply. I understood well.
Could you let me know where I can find information on
mmpbsa_py_entropy's options that can be passed from
the MMPBSA.py command-line ?
Best regards,
WATANABE
(2014/08/04 20:32), Jason Swails wrote:
>
>
>
> On Mon, Aug 4, 2014 at 6:57 AM, Hiromasa WATANABE <hi-watanabe.hpc.co.jp <mailto:hi-watanabe.hpc.co.jp>> wrote:
>
> Hi,
>
> In normal mode analysis(nmode) calculation,
> mdin is not created in spite of the -make-mdins option.
>
> According to the manual I see:
>
> 1) Call MMPBSA.py with -make-mdins like:
> $ MMPBSA.py -O -i normal_mode.in <http://normal_mode.in> -make-mdins -o normal_mode.out -cp
> T1_com.prmtop -rp T1_rec.prmtop -lp T1_lig.prmtop -y D1_com.crd.1
> 2) The user edits the mdin.
> 3) Call MMPBSA.py with -use-mdins like:
> $ MMPBSA.py -O -i normal_mode.in <http://normal_mode.in> -use-mdins -o normal_mode.out -cp
> T1_com.prmtop -rp T1_rec.prmtop -lp T1_lig.prmtop -y D1_com.crd.1
> 4) Calculation with the specified mdin will be executed.
>
> I tried MMPBSA.py in AMBER11,12 and 14.
> The mdin is created in case of &pb and &gb,
> but not in case of &nmode.
>
> How should I do to make mdin created with -make-mdins option
> in normal mode analysis(nmode) calculation?
>
>
> MMPBSA.py does not use an input file to run normal mode calculations (unlike GB and PB calculations, in
> which an input file _is_ used). MMPBSA.py calls the normal mode program (mmpbsa_py_entropy) by passing all
> input options on the command-line.
>
> Using an input file would not help much, anyway, since all relevant input variables for normal mode
> calculations are exposed via the MMPBSA.py input file. This is not the case for GB or PB calculations,
> where there are way too many options to expose to users (especially since several of them are "advanced"
> options that should not be used by the vast majority of users).
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
--
Hiromasa WATANABE
Manager, Ph.D.
HPC Dept., Technology Gr., HPC SYSTEMS Inc.
Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
Email: hi-watanabe.hpc.co.jp
www.hpc.co.jp
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Received on Mon Aug 04 2014 - 19:00:03 PDT
