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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On May 14, 2012, at 9:39 AM, Marc van der Kamp <marcvanderkamp.gmail.com> wrote: > Hi Jason, > > Thanks for the reply - I made the change and recompiled. > I don't get an error message about fort.7 not existing, but the job stops > (abruptly) after writing: > -------------------------------------------------------------------------------- > 4. RESULTS > -------------------------------------------------------------------------------- > > Again, gau_job.log is present and shows that Gaussian > has successfully finished. > The fort.7 file is not present this time (which makes sense), but the > underlying problem still persists, it appears. > Again, this is the case for tests in: > AMBERHOME/test/qmmm_EXTERN/QMMM_MD_GAUSSIAN > AMBERHOME/test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN/ > > Thanks, > Marc > > > On 14 May 2012 14:12, Jason Swails <jason.swails.gmail.com> wrote: > >> The problem seems to be that the Amber/Gaussian interface depends on all of >> the gradient information being dumped to the file "fort.7", which it claims >> will always exist. However, I'm skeptical that this is always true. >> >> Can you modify the source code and change line 600 of the file >> qm2_extern_gau_module.F90 (in $AMBERHOME/src/sander) from >> >> open(iunit, file=fortfile) !Will always exist >> >> to >> >> open(iunit, file=fortfile, status='old') !Will always exist >> >> This way, if the file doesn't exist, it will bomb out rather than create >> the file and then immediately fail to parse it. (Really, I think all of >> the file opening in the external module should use the amopen() wrapper >> rather than calling "open" directly, since it standardizes most of this >> behavior). >> >> After you do this (and recompile), do you get an error message about fort.7 >> not existing? >> >> Thanks! >> Jason >> >> On Mon, May 14, 2012 at 12:58 AM, Marc van der Kamp < >> marcvanderkamp.gmail.com> wrote: >> >>> Dear all, >>> >>> I have installed AMBER12 a little while ago, with gnu compilers gcc 4.1.2 >>> and gfortran 4.1.2 (on a cluster running Rocks 5.3, equivalent to Red Hat >>> 4.1.2-50). >>> >>> I would like to try out AMBER/Gaussian, and we have g09 as well as g03. >>> I run into problems when running the tests in >>> $AMBERHOME/test/qmmm_EXTERN/QMMM_MD_GAUSSIAN. >>> According to the mdout, Gaussian is found (in this case g09), but sander >>> fails with the following: >>> >>> SANDER BOMB in subroutine read_results (qm2_extern_gau_module) >>> Error reading file fort.7 >>> Will quit now >>> >>> gau_job.log is present and shows that Gaussian has successfully finished. >>> The fort.7 file in the directory is empty, so it is not a surprise that >> the >>> job fails. >>> But I don't know how to proceed to fix this. Any help is appreciated! >>> >>> BTW, the same error occurs when using g03 and in the pure_QM_MD_GAUSSIAN/ >>> tests. >>> >>> Many thanks, >>> Marc >>> _______________________________________________ >>> 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 >> > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon May 14 2012 - 13:00:02 PDT