Re: [AMBER] use of packmol in amber

From: M. L. Dodson <>
Date: Tue, 14 Dec 2010 08:09:19 -0600

On 12/14/2010 5:23 AM, subrata paul wrote:
> dear sir
> when i run in sander no error is coming but the output file is not written.
> thanking u
> subrata

OK, I've see this using packmol with the parameters used in their web
page examples. What is very likely (I'd say almost for sure) is that
packmol is creating a system with substantial vdw overlap (based on
the AMBER FF), and, of secondary importance, a high electrostatic
energy. This is causing NaN's during the minimization process.

If you set up the minimization to take only a few steps (and by that I
mean 1-5 steps), you may be able to get an output file to restart a
second minimization. Do a sequence of these very short minimization
runs with the output of a run being the input for the next in the
sequence. In my experience you may have to do 10 or more runs in the
sequence. Eventually, you should be able to do an ordinary

Another problem is that the packmol algorithm is packing hard spheres
with no consideration given to the orientation of the molecules. Add
in packing too close, and you will have high vdw energies plus high
electrostatic energies.

The workaround is to create a packmol system with LARGE distances
between molecules, several times the distances used in the packmol
examples. Phrased another way, do not create initial systems too
tightly packed, but then use constant pressure dynamics to during
system equilibration to equilibrate the density.

Good luck,

Bud Dodson

> On Tue, Dec 14, 2010 at 8:41 AM, Bill Ross<> wrote:
>>> My command line is
>>> $AMBERHOME/exe/sander -O -i -o min.out -p -c
>>> mixture_32.crd -r min.rst
>>> We tried it two-three times but no out put is created. Why????
>> In this situation one would expect to see a message printed by the
>> program or the operating system explaining what the problem is.
>> This is why I asked you to copy/paste the command line and the
>> result. So I expect to see something like this:
>> $ $AMBERHOME/exe/sander -O -i -o min.out -p -c
>> mixture_32.crd -r min.rst
>> AMBERHOME: Undefined variable.
>> $
>> to give one possibility. Note the presence of the two '$' shell
>> prompts - these indicate that everything from the beginning to the
>> end of program invocation have been copied and pasted. Without
>> seeing that, it is impossible to know whether you are simply
>> overlooking the diagnostic message, or whether there is no such
>> message, which would be very unusual.
>> Bill

M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email: mldodson-at-comcast-dot-net
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Received on Tue Dec 14 2010 - 06:30:03 PST
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