There has been a lot of discussion about this on the reflector in the
last few weeks.
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
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
