Re: [AMBER] use of packmol in amber

From: M. L. Dodson <>
Date: Wed, 15 Dec 2010 08:46:29 -0600

On 12/15/2010 1:13 AM, subrata paul wrote:
> Dear Sir
> I tried with your input file.But the out put file is no written.
> thanking u
> subrata

Well, I have no helpful response to that result, except maybe something
is wrong with your prmtop file. Please post the commands you used in
leap to get the prmtop and input coordinate file. Also, it might be
useful to see the start and end of the input coordinate file. If
INPUTFILE is the name of your input coordinate file, please post the
results of:




Although I can't think of a reason why this might show a problem, please
post the results of:


Bud Dodson

> On Wed, Dec 15, 2010 at 12:36 AM, M. L. Dodson<
>> wrote:
>> 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
>> &cntrl
>> imin=1, maxcyc=100,
>> ntpr=5,
>> ntr=0,
>> /
>> ---------------
>> 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
Received on Wed Dec 15 2010 - 07:00:03 PST
Custom Search