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
>
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Received on Mon Jan 24 2011 - 23:30:01 PST
