Re: [AMBER] MMPBSA problems with Fe and Zn

From: Jason Swails <>
Date: Mon, 1 Mar 2010 09:07:53 -0500


On Mon, Mar 1, 2010 at 7:00 AM, mattia <> wrote:
> Hi,
> You should insert Zinc parameters into the file that
> is in the $AMBERHOME/src/mm_pbsa/ directory.
> If I don't remember bad you should only insert wdv radius and solvation of
> Zinc ion.
> Then you have, however, to recompile the mm_pbsa module (or maybe the whole

Perl is an interpreted/scripting language that doesn't require
"compilation" in the traditional sense. Editing a perl module should
not require a re-compilation of either Amber or If you
edit a .pl script (instead of .pm), it's slightly more complex. All
of the .pl scripts contain two copies: the one in $AMBERHOME/bin and
the one in $AMBERHOME/src/mm_pbsa, that should be identical. Thus, if
you have to make changes to one of them, you should change the one in
$AMBERHOME/src/mm_pbsa and run "make install" in that directory to
replace the one in $AMBERHOME/bin with the one you edited in
$AMBERHOME/src/mm_pbsa. However, for a .pm module, it should be
sufficient to edit the file and simply use it.

> Before to do that you could try with the new I don't know how it
> works with Zinc, maybe it is more "user friendly" than the old MM_PBSA perl

It takes the Zinc radius from the prmtop file. It does this because
there is no option to use molsurf, which would require an external
definition of the radius. However, results with/without molsurf
differ only very slightly in my experience. I believe also
has an option to do this, though I'm not familiar enough with using
that version to speak definitively on it.

> script.
> Regards
> Mattia

Good luck!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Mon Mar 01 2010 - 06:30:03 PST
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