very very thank you.
Mininization is going well.
thank you
subrata
On Tue, Jan 25, 2011 at 11:29 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jan 25 2011 - 02:00:04 PST
