Hi Jason,
Thanks again for your reply.
The line says "NETCDF=netcdf.mod"
It's interesting that you mention running the tests by hand. That's what I'd
been doing when I'd gotten the error about not having netCDF support.
However, when I ran /usr/local/amber11/AmberTools/test/test_in_serial.sh,
it seemed that a lot of the tests that had failed when I ran them by hand,
ended up passing. I've attached the log from this run if you or anyone else
wants to have a look at it. I usually only use tleap, ambpdb and ptraj from
AmberTools, but these seem to be okay.
I also have a few more questions.
In /usr/local/amber11/test/, there is only ndiff.awk. Should there be as
many files here as there are in /usr/local/amber11/AmberTools/test/? If this
is the case, would it be best for me to recompile?
Is there any documentation regarding what each file in the test directory
actually does?
In my compiled version of AmberTools, in
/usr/local/amber11/AmberTools/test/sleap, I have a lot of subdirectories
like addions, amoeba and prmtop, while the general
/usr/local/amber11/AmberTools/test/leap
directory doesn't have that. Is that normal?
Is there a difference between using the modules in /usr/local/amber11/exe/
vs. those in /usr/local/amber11/AmberTools/exe/?
I'm sorry if I'm asking questions that have been answered elsewhere in the
AMBER mailing list archive or in the documentation. Please let me know if
this is the case and I would be happy to look for the answers there.
Thank you all,
Kamali Sripathi
On Sun, May 8, 2011 at 12:24 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Sun, May 8, 2011 at 3:53 PM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
>
> > Hi Jason,
> >
> > Thanks a lot for your reply.
> >
> > On Sun, May 8, 2011 at 8:56 AM, Jason Swails <jason.swails.gmail.com>
> > wrote:
> >
> > >
> > > > Is it a problem that ptraj was not built with NetCDF support?
> > > >
> > >
> > > Only if you want to process NetCDF trajectories. Is there a reason you
> > > compiled without NetCDF support? (You have to go out of your way to
> omit
> > > NetCDF support).
> >
> >
> > That's actually the part that was confusing me, because as far as I could
> > tell, I did compile AmberTools with NetCDF support, but for some reason,
> > ptraj doesn't accept it.
> >
> > Configuring NetCDF; (may be time-consuming)
> >
> > NetCDF configure succeeded.
> >
> > As far as I know, my trajectories are formatted, because I don't set the
> > ioutfm variable. Would the lack of NetCDF support still be a problem in
> > this
> > case?
> >
>
> Oh. What does your config.h file look like? What does the line that
> starts
> with "NETCDF=" say?
>
> You could also try to run those specific tests by hand to see if they pass
> (because it might be fine).
>
> HTH,
> Jason
>
>
> > Thank you, and sorry for repetitious questions.
> >
> > Kamali Sripathi
> >
> > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> >
> >
> > --
> > Kamali Sripathi
> > Graduate Student, Medicinal Chemistry
> > Walter Laboratory
> > 930 North University
> > Ann Arbor, MI, 48109
> > ksripath.umich.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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Received on Mon May 09 2011 - 11:30:04 PDT
