Re: [AMBER-Developers] Testing Periodic ICCG pbsa solver under MMPBSA

From: Jason Swails <>
Date: Tue, 19 Feb 2013 18:08:53 -0500

On Tue, Feb 19, 2013 at 5:34 PM, <> wrote:

> I have tried using the -make-mdins and -use-mdins options with .
> As suggested, I generated the .mdin files using -make-mdins. I then modify
> the values for the bcopt and solvopt flags under the .mdin file generated
> for the pb run as needed. Then I ran again using -use-mdins.
> As expected, the gb ran normally.
> Unfortunately, when the program hits the pb run a new (but very similar)
> error message appears:
> "Error: mm_option: unknown keyword or invalued value: solvopt"
> It looks like there is another check or something that is blocking use of
> the solvopt and bcopt values needed.
> Do you have any idea what I would need to change so I can get it to run?

You need to modify the NAB interface as well. At the very least, you have
to adjust the flex-based input parser to accept the new values. Look in
$AMBERHOME/AmberTools/src/sff/mm_options.l -- you will have to adjust
solvopt to accept 8 and bcopt to accept 1's and 0's.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Tue Feb 19 2013 - 15:30:04 PST
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