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 - 14:31:56 CDT

Carlos and all,

Thanks, Carlos, for the pointer -- I was getting nothing out, still,
as I had ntwx=0.

Now it seems to be actually reprocessing my trajectories, but
everything gets written to mdout. Is there any way I can get it to
still write energies to the energy file? Obviously this is not crucial
as I can just extract from the mdout if necessary, but it would be
cleaner if they would go into the energy file.

Thanks,
David

On 4/10/07, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
> sorry I've been traveling almost continuously for a few weeks and have
> not been back long enough to get this in. in the meantime
> make sure to set ntwx>0 or it won't open the traj file.
> it is correct that in the current version you use -x for the input
> traj and cannot get an output traj. sorry for the delays, when I
> am back in the lab for more than a couple days I will get this done.
> carlos
>
> 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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