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
Received on Mon Jan 24 2011 - 07:00:04 PST
