Re: [AMBER] use of packmol in amber

From: subrata paul <paul.subrata34.gmail.com>
Date: Tue, 14 Dec 2010 07:57:29 +0400

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
>
>
> _______________________________________________
> 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 Dec 13 2010 - 20:00:03 PST
Custom Search