Thread: Re: [Apbs-users] Outputfile with APOLAR calculations
Biomolecular electrostatics software
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From: Nathan B. <ba...@cc...> - 2008-05-20 11:16:37
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Hello -- This example ran on my computer with the attached output. What version of APBS are you using? Thanks, Nathan On May 20, 2008, at 5:23 AM, François BAGAINI wrote: > Hello Nathan, > Here are my files. I have used OPLS parameters because it was easier > for me but I'm working on Amber parameters for further calculations. > Thanks for your help. > Francois > > > > > > > Message du 20/05/08 03:13 > > De : "Nathan Baker" > > A : "bagaini.fr" > > Copie à : apb...@li... > > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > > > Hello -- > > > > Can you please send the input file and PQR so we can know a bit more > about the setup of your system? > > > > Thanks, > > > > Nathan > > > > On May 19, 2008, at 2:50 PM, bagaini.fr wrote: > > Hi, > I use APBS on a windows XP plateform. I have performed ELEC > calculations with an outputfile specification to write the results > in a file. But when I do the same with APOLAR settings the file is > created, the date and time are written in the file...and that all! > What should I have done? > Thanks a lot for your help. > Francois > ------------------------------------------------------------------------- > > This SF.net email is sponsored by: Microsoft > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________ > > apbs-users mailing list > > apb...@li... > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > > > > > > > > > > <1dlhAPO.in><1dlh_pep.pqr><1dlh.pqr><oplsP.prm> -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: François B. <bag...@wa...> - 2008-05-21 19:29:24
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hello, I use the version 1.0.0. I get the same results as yours, but written on my console not in the file I have specified with the --outputfile=1dlhAPO.out option. Kind regards Francois > Message du 20/05/08 13:16 > De : "Nathan Baker" > A : "François BAGAINI" > Copie à : apb...@li... > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > Hello -- > > This example ran on my computer with the attached output. What > version of APBS are you using? > > Thanks, > > Nathan > > > > On May 20, 2008, at 5:23 AM, François BAGAINI wrote: > > > Hello Nathan, > > Here are my files. I have used OPLS parameters because it was easier > > for me but I'm working on Amber parameters for further calculations. > > Thanks for your help. > > Francois > > > > > > > > > > > > > Message du 20/05/08 03:13 > > > De : "Nathan Baker" > > > A : "bagaini.fr" > > > Copie à : apb...@li... > > > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > > > > > Hello -- > > > > > > > Can you please send the input file and PQR so we can know a bit more > > about the setup of your system? > > > > > > > Thanks, > > > > > > > Nathan > > > > > > > On May 19, 2008, at 2:50 PM, bagaini.fr wrote: > > > > Hi, > > I use APBS on a windows XP plateform. I have performed ELEC > > calculations with an outputfile specification to write the results > > in a file. But when I do the same with APOLAR settings the file is > > created, the date and time are written in the file...and that all! > > What should I have done? > > Thanks a lot for your help. > > Francois > > ------------------------------------------------------------------------- > > > This SF.net email is sponsored by: Microsoft > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________ > > > apbs-users mailing list > > > apb...@li... > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > > > > -- > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > > Center for Computational Biology, Washington University in St. Louis > > Web: http://cholla.wustl.edu/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <1dlhAPO.in><1dlh_pep.pqr><1dlh.pqr> > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > > > [ (pas de nom de fichier) (0.0 Ko) ] |
From: Nathan B. <ba...@cc...> - 2008-05-21 19:38:55
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Hello -- The --output-file option is a bit misleading. It was designed for specific logging of information for use in web server/services applications. The best way to capture APBS output is by redirecting the stdout on the console. If you're using BASH, this would be something like $ apbs file.in > file.out or $ apbs file.in | tee file.out Sorry for the confusion. -- Nathan On May 21, 2008, at 2:28 PM, François BAGAINI wrote: > hello, > I use the version 1.0.0. I get the same results as yours, but > written on my console not in the file I have specified with the -- > outputfile=1dlhAPO.out option. > Kind regards > Francois > > > > > > Message du 20/05/08 13:16 > > De : "Nathan Baker" > > A : "François BAGAINI" > > Copie à : apb...@li... > > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > > > Hello -- > > > > This example ran on my computer with the attached output. What > > version of APBS are you using? > > > > Thanks, > > > > Nathan > > > > > > > > On May 20, 2008, at 5:23 AM, François BAGAINI wrote: > > > > > Hello Nathan, > > > Here are my files. I have used OPLS parameters because it was > easier > > > for me but I'm working on Amber parameters for further > calculations. > > > Thanks for your help. > > > Francois > > > > > > > > > > > > > > > > > > > Message du 20/05/08 03:13 > > > > De : "Nathan Baker" > > > > A : "bagaini.fr" > > > > Copie à : apb...@li... > > > > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > > > > > > > Hello -- > > > > > > > > > > Can you please send the input file and PQR so we can know a bit > more > > > about the setup of your system? > > > > > > > > > > Thanks, > > > > > > > > > > Nathan > > > > > > > > > > On May 19, 2008, at 2:50 PM, bagaini.fr wrote: > > > > > > Hi, > > > I use APBS on a windows XP plateform. I have performed ELEC > > > calculations with an outputfile specification to write the results > > > in a file. But when I do the same with APOLAR settings the file is > > > created, the date and time are written in the file...and that all! > > > What should I have done? > > > Thanks a lot for your help. > > > Francois > > > > ------------------------------------------------------------------------- > > > > This SF.net email is sponsored by: Microsoft > > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________ > > > > apbs-users mailing list > > > > apb...@li... > > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > > > > > > > > > > -- > > > Associate Professor, Dept. of Biochemistry and Molecular > Biophysics > > > Center for Computational Biology, Washington University in St. > Louis > > > Web: http://cholla.wustl.edu/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <1dlhAPO.in><1dlh_pep.pqr><1dlh.pqr> > > > > -- > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > > Center for Computational Biology, Washington University in St. Louis > > Web: http://cholla.wustl.edu/ > > > > > > > > > > > > > > > > [ (pas de nom de fichier) (0.0 Ko) ] -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: François B. <bag...@wa...> - 2008-05-22 12:29:36
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hello, Ok it does work. Thanks a lot for your usefull application and for your help. regards Francois > Message du 21/05/08 21:38 > De : "Nathan Baker" > A : "François BAGAINI" > Copie à : apb...@li... > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > Hello -- > > The --output-file option is a bit misleading. It was designed for > specific logging of information for use in web server/services > applications. The best way to capture APBS output is by redirecting > the stdout on the console. If you're using BASH, this would be > something like > > $ apbs file.in > file.out > > or > > $ apbs file.in | tee file.out > > Sorry for the confusion. > > -- Nathan > > On May 21, 2008, at 2:28 PM, François BAGAINI wrote: > > > hello, > > I use the version 1.0.0. I get the same results as yours, but > > written on my console not in the file I have specified with the -- > > outputfile=1dlhAPO.out option. > > Kind regards > > Francois > > > > > > > > > > > Message du 20/05/08 13:16 > > > De : "Nathan Baker" > > > A : "François BAGAINI" > > > Copie à : apb...@li... > > > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > > > > > Hello -- > > > > > > This example ran on my computer with the attached output. What > > > version of APBS are you using? > > > > > > Thanks, > > > > > > Nathan > > > > > > > > > > > > On May 20, 2008, at 5:23 AM, François BAGAINI wrote: > > > > > > > Hello Nathan, > > > > Here are my files. I have used OPLS parameters because it was > > easier > > > > for me but I'm working on Amber parameters for further > > calculations. > > > > Thanks for your help. > > > > Francois > > > > > > > > > > > > > > > > > > > > > > > > > Message du 20/05/08 03:13 > > > > > De : "Nathan Baker" > > > > > A : "bagaini.fr" > > > > > Copie à : apb...@li... > > > > > Objet : Re: [Apbs-users] Outputfile with APOLAR calculations > > > > > > > > > > Hello -- > > > > > > > > > > > > > Can you please send the input file and PQR so we can know a bit > > more > > > > about the setup of your system? > > > > > > > > > > > > > Thanks, > > > > > > > > > > > > > Nathan > > > > > > > > > > > > > On May 19, 2008, at 2:50 PM, bagaini.fr wrote: > > > > > > > > Hi, > > > > I use APBS on a windows XP plateform. I have performed ELEC > > > > calculations with an outputfile specification to write the results > > > > in a file. But when I do the same with APOLAR settings the file is > > > > created, the date and time are written in the file...and that all! > > > > What should I have done? > > > > Thanks a lot for your help. > > > > Francois > > > > > > ------------------------------------------------------------------------- > > > > > This SF.net email is sponsored by: Microsoft > > > > > Defy all challenges. Microsoft(R) Visual Studio 2008. > > > > > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/_______________________________________________ > > > > > apbs-users mailing list > > > > > apb...@li... > > > > > https://lists.sourceforge.net/lists/listinfo/apbs-users > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > Associate Professor, Dept. of Biochemistry and Molecular > > Biophysics > > > > Center for Computational Biology, Washington University in St. > > Louis > > > > Web: http://cholla.wustl.edu/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > <1dlhAPO.in><1dlh_pep.pqr><1dlh.pqr> > > > > > > -- > > > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > > > Center for Computational Biology, Washington University in St. Louis > > > Web: http://cholla.wustl.edu/ > > > > > > > > > > > > > > > > > > > > > > > > [ (pas de nom de fichier) (0.0 Ko) ] > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > > > > |