Re: [AMBER] Problem with MMPBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 11 Nov 2015 08:27:42 -0500

On Wed, Nov 11, 2015 at 8:18 AM, Soong Jiaxin <jiaxinsoong.gmail.com> wrote:

> I did provide the same MMPBSA.py input file when I ran the make-mdin file.
>

​No you did not.​ You said your command was

MMPBSA.py -i _MMPBSA_gb.mdin ... -use-mdins

In this case, you provided _MMPBSA_gb.mdin as the input file. This file
should not have existed when you ran MMPBSA.py with the -make-mdins flag.
If you do

MMPBSA.py -i mmpbsa.in ... -make-mdins

​then your next command, after editing the _MMPBSA_gb.mdin file as you need
to, should be

MMPBSA.py -i mmpbsa.in ... -use-mdins​

The _MMPBSA_gb.mdin is the resultant file. Do you mean that the correct
> program to be used for this newly created _MMPBSA_gb.mdin file should be
> sander instead of MMPBSA.py?
>

M
​MPBSA.py will call sander automatically. If you specify -use-mdins, then
MMPBSA.py will *not* create its own _MMPBSA_gb.mdin file and instead will
use the one that already exists.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Nov 11 2015 - 05:30:10 PST
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