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
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Received on Mon Jan 24 2011 - 07:30:02 PST
