Re: [AMBER-Developers] Tests Errors in AmberTools

From: Claudia Ramírez <claudia.lilian.ramirez.gmail.com>
Date: Thu, 9 Jun 2016 15:30:33 -0300

Hi again,

So, I did a pull today, and there is no more error with pytraj, but I keep
having two regarding the QM/MM periodic interface (Testing the QM/MM
periodic interface (PM3-PDDG) // SANDER BOMB in subroutine
qmtheorymodule:SetQmTheoryType // Unknown method specified for qm_theory ),
and the error with my variable (drar) on the QM/MM non-periodic interface
in sanderapi, that last week wasn't there.

I'm attaching the new log file.

Thanks

2016-06-09 1:12 GMT-03:00 Hai Nguyen <nhai.qn.gmail.com>:

> On Wed, Jun 8, 2016 at 1:40 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > Looking at the log, I think Claudia used system python:
> >
> > > /usr/bin/python test.py
> >
> > I agree that we should always suggest users to install miniconda (with
> Y/N)
> >
> I will go ahead make that change. If anyone has strong objection, please
> > reply here. thanks.
> >
> >
> So I just made the change to master branch. Please have a test and let me
> know if I need to update anything.
> If anyone wants to use his/her own Python, simply saying 'N'.
>
> Cheers
>
> Hai
>
> Hai
> >
> > On Wed, Jun 8, 2016 at 1:33 PM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >> On Wed, Jun 08, 2016, Claudia Ramírez wrote:
> >> >
> >> > I did a git pull on Monday (June 6), with gnu 4.8 compilers and doing
> >> just
> >> > ./configure gnu (serial for now) in Ubuntu 14.04 LTS. And it has 4
> >> tests on
> >> > AmberTools that aren't working (this is without my modifications),
> and I
> >> > don't know why. I'm attaching the log file to see if anyone could help
> >> me
> >> > make it work.
> >>
> >> All the problems are python-related problems, related either to pytraj
> or
> >> to the sander api interface.
> >>
> >> What is the PYTHON variable in your config.h? If you are not already
> >> using a miniconda python, try going to $AMBERHOME/AmberTools/src and
> >> running
> >> configure_python. Then go back to AMBERHOME and re-run configure.
> >>
> >> [I still am pushing the (so-far, minority) viewpoint that all users
> should
> >> be offered the choice to install the miniconda python. Users that have
> >> both
> >> experience with python, and the desire/need to use a different
> >> interpreter,
> >> are welcome to decline the offer. But configure2 is still prone to
> >> deciding
> >> that the python in a user's path is OK when it is in fact not OK. So,
> >> letting
> >> us know which python your Amber installation is using would be a help
> >> here.]
> >>
> >> ....dac
> >>
> >>
> >> _______________________________________________
> >> AMBER-Developers mailing list
> >> AMBER-Developers.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber-developers
> >>
> >
> >
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Received on Thu Jun 09 2016 - 12:00:03 PDT
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