AMBER Archive (2007)

Subject: Re: AMBER: sander (AMBER 9) and -y flag -- not working?

From: David Mobley (dmobley_at_gmail.com)
Date: Tue Apr 10 2007 - 14:04:52 CDT

Sorry, I take my last note back. I had failed to adjust nrespa for
minimization, so I was just getting an error in mdout.

Thanks,
David

On 4/10/07, David Mobley <dmobley_at_gmail.com> wrote:
> Chris,
>
> > There has been a lot of discussion about this on the reflector in the
> > last few weeks.
>
> Thanks for responding anyway!
>
> I've looked at the old discussion, which apparently was concluded by
> Carlos Simmerling saying he was going to post a bugfix. I also found a
> note on the manual page that says to use -x instead of -y, as you're
> suggesting. However, see below.
>
> > 1) Use -x to specify the stored coordinate file. (I'd write protect the
> > trajectory file first just to be triple sure!)
> >
> > 2) Note the stored coordinates must be in ASCII format. Netcdf is not
> > supported by IMIN=5
> >
> > 3) Note that the energies you get will be "off" from your original
> > energies as the original energies printed out are for the frames
> > immediately prior to the frames output in the trajectory file.
> >
> > All of this was discussed in last week or two.
> >
> > Here is a command that might get you going:
> >
> > sander -O \
> > -p prmtop\
> > -o energies.out \
> > -i energyscan.in \
> > -x trajectory.crd
>
> So, I'm trying this now, and I'm not getting anything out. I tried
> with ntwe set to the original value, and ntwe=1. Is it working for
> you?
>
> Thanks,
> David
>
>
> >
> >
> > David Mobley wrote:
> > > All,
> > >
> > > I'm trying to use the -y flag of Sander, as described on pages 87 and
> > > 90 of the AMBER 9 manual, to evaluate certain energies of a stored
> > > trajectory using slightly modified run parameters. I've set imin=5.
> > > However, Sander complains that -y is an unknown flag.
> > >
> > > Is the -y flag obsolete, or is there a bug, or...?
> > >
> > > Thanks,
> > > David
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