Re: [AMBER] -make-mdins does not work with nmode

From: Hiromasa WATANABE <>
Date: Tue, 05 Aug 2014 10:55:23 +0900

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 command-line ?

Best regards,

(2014/08/04 20:32), Jason Swails wrote:
> On Mon, Aug 4, 2014 at 6:57 AM, Hiromasa WATANABE < <>> 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 with -make-mdins like:
> $ -O -i <> -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 with -use-mdins like:
> $ -O -i <> -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 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?
> does not use an input file to run normal mode calculations (unlike GB and PB calculations, in
> which an input file _is_ used). 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 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

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.
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Received on Mon Aug 04 2014 - 19:00:03 PDT
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