Re: [AMBER] disable minimization in nmode MMPBSA.py

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 15 May 2015 18:07:03 -0400

On Fri, May 15, 2015 at 5:02 PM, Carlos Modenutti <cpmode.gmail.com> wrote:

> Hi,
>
> I need to calculate the normal mode entropy for a series of complexes.
> For that aim, I'm developping a new method that performs the minimization
> outside of mmpbsa.py, and therefore I need to disable this minimization
> step within &nmode itself.
> I've tried using maxcyc=0, but it didn't work since it needs a positive
> integer in this variable.
>

‚ÄčSimplest way I can think of is to disable it inside mmpbsa_entropy.nab
itself. If you comment out lines 69 and 100 (the calls to "xmin"), the
minimization step should be skipped. (Then, of course, reinstall MMPBSA.py,
which should be as simple as running "make install" inside the
$AMBERHOME/AmberTools/src/mmpbsa_py directory after configuring in serial.)

That said, if you are doing ‚Äčthe minimization outside of MMPBSA.py,
shouldn't you already be close to a minimum? That is unless you're using a
different Hamiltonian to minimize, in which case your minimization won't
get you to the point where your low-frequency modes are accurate (or even
real).

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri May 15 2015 - 15:30:02 PDT
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