Re: [AMBER] use of packmol in amber

From: M. L. Dodson <>
Date: Tue, 14 Dec 2010 13:06:18 -0600

Following up on my own posting. From prodding by Bill Ross, I was
wrong about the no output symptom. I think I was confusing two
different results from my packmol investigations (serves me right
posting from memory). Without searching really hard, I THINK I remember
the no output symptom is from specifying the wrong type of input file.

Try the following mdin file:

Minimization with NO Cartesian restraints
 imin=1, maxcyc=100,

You should get some output, but then the minimization will probably
fail with a segmentation fault. If it does, just do the sequence
of short minimizations I posted (below). If the minimization goes
for maxcyc=100 steps, you should be able to proceed along as normal.

Good luck!

Bud Dodson

On Dec 14, 2010, at 8:09 AM, M. L. Dodson wrote:

> 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
> minimization.
> 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
> Mobile Phone: eight_three_two-56_three-386_one
> _______________________________________________
> AMBER mailing list

M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Tue Dec 14 2010 - 11:30:04 PST
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