[AMBER] MMPBSA.py -make-mdins does not work with nmode

From: Hiromasa WATANABE <hi-watanabe.hpc.co.jp>
Date: Mon, 04 Aug 2014 19:57:36 +0900

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?

Best regards,
WATANABE

-- 
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 04 2014 - 04:30:02 PDT
Custom Search