Hi
check whether all the parameters are fit in the system using xleap. and
also check for the co-ordinates as it should be different for each molecule
of trehalose, then try to run
all the best
With Regards
Gopalakrishnan.R
On Tue, Dec 14, 2010 at 9:27 AM, subrata paul <paul.subrata34.gmail.com>wrote:
> Dear sir
>
> At first we make waterPDB and trhalosePDB .
> then by using PACKMOL we make a PDB file for 10 trehalose and 1000 water
> with cubic box(input file is attach herewith).
> After making this PDB , we load in XLEAP in amber 10 using GLYCAM _06
> force field.
> after loading the PDB file , we save the xxx.top and xxx.crd
> (saveamberparm xxx xxx.top xxx.crd) .
> Then we tried for initial minimization(input is attach herewith) by sander
> command in amber10
> but the output file is not created (eg. min.out ,min.rst). WHY?????
> How we solve the problem , Where is going wrong???
>
>
> thanking you
> subrata
> On Mon, Dec 13, 2010 at 4:43 PM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Mon, Dec 13, 2010, subrata paul wrote:
> > >
> > > We make a pdb file for 10 trehalose and 1000 water molecules(cubic box)
> > by
> > > PACKMOL. we use ter card in packmol.
> > > >From that pdb file we make top and crd file in XLEAP (amber10).
> > > Then we tried for initial minimization
> > > *min.in
> > > *&cntrl
> > > imin=1,
> > > maxcyc=500,
> > > ncyc=250,
> > > ntb=1,
> > > ntr=0,
> > > cut=15.0
> > > /
> > >
> > > but the output file is not created.
> >
> > We need more information. First, the *exact* input file; if you really
> > have
> > "*&cntrl" in your file, then it won't work. Second, the command line you
> > used. Third, what happened? (e.g. you immediately got a new prompt;
> there
> > was some message on the command line, etc.)
> >
> > Not getting any output at all probably has nothing to do with packmol.
> Do
> > other Amber jobs run correctly?
> >
> > ...dac
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
--
GOPALAKRISHNAN.R
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Received on Mon Dec 13 2010 - 21:00:04 PST
