Re: [AMBER] Problem with MMPBSA

From: Jason Swails <>
Date: Wed, 11 Nov 2015 08:27:42 -0500

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

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

​No you did not.​ You said your command was -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 with the -make-mdins flag.
If you do -i ... -make-mdins

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

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


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