Re: [AMBER] mmpbsa doesn't work

From: Billy Miller III <>
Date: Tue, 23 Mar 2010 09:22:55 -0400

Just looking at your input file, it does not look like you told the program
to run any calculations. You told it the prmtop name and to only do
calculations on the complex, but you never specified what type of
calculation (GC, AS, DC, MM, GB, PB, MS, or NM) to perform in the .GENERAL
section. You gave it parameters for GB, but never turned GB on by setting it
to 1 in the .GENERAL section. Furthermore, have you already generated
snapshots? This is not apparent from you still specifying the trajectory
file, which needs to be in a .TRAJECTORY section, also. will not
perform post-process analysis on a trajectory alone, you will need to create
snapshots first (which can be done setting GC to 1 in the .GENERAL section).
The input file actually looks a lot like a cross between the inputs used for and See the AMBER Manual or MM/PBSA tutorial ( for more specifics on this
type of calculation.

Good luck!

-Bill Miller

On Mon, Mar 22, 2010 at 11:38 PM, qiaoyan <> wrote:

> Hello, everone, I want to use mmpbsa to calculate the hydrophobic and
> hydrophilic surface area, the script I write don't work, the input file and
> output file are attached.
> Best Regards.
> Yours sincerely,
> Yan Qiao.
> 2010-03-23
> -----------------------------------------------
> State Key Lab of Molecular Reaction Dynamics (SKLMRD),
> Dalian Institute of Chemical Physics(DICP),
> the Chinese Academy of Sciences(CAS),
> Zhongshan Road457, Dalian City,
> Liaoning Province 116023,P. R. China
> E-mail:
> Office Phone: +86+411+84379352
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Received on Tue Mar 23 2010 - 06:30:04 PDT
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