Your leap script was not set up for periodic simulations.
Try using the "setbox" command in leap. I think it is documented in the
user manual.
Good luck!
Jason
On Tue, Jan 25, 2011 at 2:18 AM, subrata paul <paul.subrata34.gmail.com>wrote:
> Dear Sir,
> For Minimization the command is
> $ABERHOME/exe/sander -O -i min.in -o min.out -p tre10.prmtop -c
> tre10.inpcrd -r min.rst
>
> In the tre10.prmtop file this three flags are mising
> %FLAG SOLVENT_POINTERS
> %FLAG ATOMS_PER_MOLECULE
> %FLAG BOX_DIMENSION
> %FORMAT(5E16.8)
> and nobox information in the tre10.inpcrd file
>
> why this is happen?
> How it can be solve?
>
> thanking you
> subrata
> On Mon, Jan 24, 2011 at 7:17 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > Hello,
> >
> > In order to diagnose your problem, though, we most likely need more
> > information. What exact commands did you try? What does your topology
> > file
> > look like? etc.
> >
> > It could be that your system is so large that it's taking awhile to do
> > anything. You could also try looking through some of the test cases that
> > test minimization of the type you're doing and using that mdin file (and
> > adapting some of the input parameters to match what you're trying to do).
> >
> > Good luck,
> > Jason
> >
> > On Mon, Jan 24, 2011 at 9:47 AM, subrata paul <paul.subrata34.gmail.com
> > >wrote:
> >
> > > Dear sir
> > >
> > > I make a pdb file for my trehalose concentration. and converted into
> > prmtop
> > > and inpcrd file using xleap -f leaprc.GLYCAM_06 command.
> > > After that i tried to minimize in amber 10. but when i tried to
> minimize
> > > with following input by sander it takes to many time ,does not showing
> > any
> > > error, when i put sander comman it remains as it is. why does it
> > happening?
> > > min.in
> > > &cntrl
> > > imin=1,
> > > maxcyc=150,
> > > ncyc= 50,
> > > cut=10,
> > > /
> > > How i solve this problem?
> > > thanking you
> > > subrata
> > >
> > >
> > > On Mon, Jan 24, 2011 at 6:19 PM, Lachele Foley (Lists) <
> > lf.list.gmail.com
> > > >wrote:
> > >
> > > > In addition to what Jason said, yes, that is correct for trehalose.
> > > > Of course, we always recommend opening the prmtop and inpcrd in vmd
> to
> > > > make sure the molecule looks right. Just don't forget for Amber 10
> to
> > > > use scee=1 and scnb=1 in your control file.
> > > >
> > > > :-) Lachele
> > > >
> > > > On Mon, Jan 24, 2011 at 7:17 AM, Jason Swails <
> jason.swails.gmail.com>
> > > > wrote:
> > > > > You could save a PDB of the trehalose molecule and use packmol to
> > > create
> > > > a
> > > > > solvent box of trehalose and water around your desired solute in
> the
> > > > proper
> > > > > proportions. Knowing the experimental density would probably help.
> > > They
> > > > > key is just to put the proper number of molecules in a given volume
> > of
> > > > > solution.
> > > > >
> > > > > Due to the pure massiveness of the mole, lower concentrations will
> be
> > > > more
> > > > > difficult to simulate.
> > > > >
> > > > > Hope this helps,
> > > > > Jason
> > > > >
> > > > > On Mon, Jan 24, 2011 at 12:58 AM, subrata paul <
> > > paul.subrata34.gmail.com
> > > > >wrote:
> > > > >
> > > > >> Dear sir
> > > > >>
> > > > >> I want to simulate 1-6M trehalose solution in amber10.
> > > > >>
> > > > >> In xleap -f leaprc.GLYCAM_06
> > > > >> trehalose=sequence {1GA 0GA}
> > > > >> Is this ok for makeing trehalose ?
> > > > >>
> > > > >>
> > > > >> How i make 1 - 6 Molar concentration of trehalose solution?
> > > > >>
> > > > >>
> > > > >> thanking you
> > > > >> subrata
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
> > > > >> AMBER.ambermd.org
> > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jason M. Swails
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Graduate Student
> > > > > 352-392-4032
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > :-) Lachele
> > > > Lachele Foley
> > > > CCRC/UGA
> > > > Athens, GA USA
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Jan 25 2011 - 00:00:05 PST
