Jason and Bergy,
Thank you both for your replies. I have checked the *prm file for tabs and
have looked for any idiosyncrasies in the bond parameter table that might
cause chamber to misread. So far, I have not identified the problem, but I
am still looking. I will also try the new patch to see if it resolves the
issue.
Sally
On Thu, Feb 21, 2013 at 5:25 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Wed, Feb 20, 2013 at 11:49 PM, BERGY <nucleic81.gmail.com> wrote:
>
> > Hi Sally,
> > Pls check if the file has some tabs in it. i had a similar problem. had
> to
> > replace the tabs with space in the prm files
> >
>
> Ah. I see that, indeed, tabs would cause an issue like this. If you still
> have one of those PSFs with tabs around, can you try this patch to see if
> it fixes that behavior?
>
> You can apply it by going to AMBERHOME and typing:
>
> patch -p0 -N < chamber.patch
>
> Then you'll have to re-compile chamber (which you can do rapidly by going
> to $AMBERHOME/AmberTools/src/chamber and typing "make install".
>
> Thanks!
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
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Received on Thu Feb 21 2013 - 09:00:02 PST
