Dear Sir
I tried with your input file.But the out put file is no written.
thanking u
subrata
On Wed, Dec 15, 2010 at 12:36 AM, M. L. Dodson <
activesitedynamics.comcast.net> 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<ross.cgl.ucsf.edu> wrote:
> >>
> >>>> My command line is
> >>>> $AMBERHOME/exe/sander -O -i min.in -o min.out -p mixture_32.top -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 min.in -o min.out -p mixture_32.top -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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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 - 23:30:03 PST
