AMBER Archive (2009)

Subject: Re: [AMBER] Is it the way to do simulation in vacuum

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Oct 30 2009 - 08:26:20 CDT

have you run the test cases?

On Fri, Oct 30, 2009 at 7:11 AM, nicholus bhattacharjee <
nicholusbhattacharjee_at_gmail.com> wrote:

> On Fri, Oct 30, 2009 at 6:21 AM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
> > we need to see your sander input.
> > also- what does your sander run script look like? if you do a "top" on
> that
> > machine, is sander still running?
> >
> > Dear community,
> > > I am trying to simulate my protein in vacuum.
> I
> > am
> > > preparing the topology and parameter files as follows
> > >
> > > $ tleap
> > > > source leaprc.ff99SB
> > > > mol=loadpdb pdb
> > > > saveamberparm mol prmtop inpcrd
> > > >quit
> > >
> > > Then I have run the minimization of 250 cycles. But this small
> > minimization
> > > is not coming out. And investigating the output file by "tail -f"
> command
> > > only shows the following
> > > --------------------------------------------
> > > AMBER 9 SANDER 2006
> > > --------------------------------------------
> > >
> > > I am unable to find the defect in the procedure. Please help.
> > >
> > > --
> > > Nicholus Bhattacharjee
> > > PhD Scholar
> > > Department of Chemistry
> > > University of Delhi
> > > Delhi-110007 (INDIA)
> > > Phone: 9873098743(M)
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> The input file is
>
> Minimization of the entire molecular system
> &cntrl
> imin=1, maxcyc=250,
> ntpr=5,
> &end
>
>
> I am running sander as
>
> $ sander -O -i inputfile -p prmtop -c inpcrd -o outputfile -r restrtfile
>
> Yes sander is running when when I top. By the way do I have to make ntb=0
> in
> the input file?
> --
> Nicholus Bhattacharjee
> PhD Scholar
> Department of Chemistry
> University of Delhi
> Delhi-110007 (INDIA)
> Phone: 9873098743(M)
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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