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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Received on Wed Apr 11 2007 - 06:07:42 PDT
