AMBER Archive (2009)

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

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Fri Oct 30 2009 - 06:11:03 CDT

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
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>

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)
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