On Mon, Aug 4, 2014 at 6:57 AM, Hiromasa WATANABE <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 -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 -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
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Received on Mon Aug 04 2014 - 05:00:02 PDT
