thanks. It was able to generate the needed files as indicated in the tutorial. I trnasfered my working directory. many thanks. Bernard
--- On Wed, 2/2/11, Justin A. Lemkul <jalem...@vt.edu> wrote: From: Justin A. Lemkul <jalem...@vt.edu> Subject: Re: [gmx-users] luck To: "Gromacs Users' List" <gmx-users@gromacs.org> Date: Wednesday, February 2, 2011, 2:32 AM Mr Bernard Ramos wrote: > > this is the command i am using: > pbd2gmx -f 1AKI.pdb -o 1AKI_processed.gro -water spce > then I choose a force fileld. > then I get the error and no new files generated at all. > My working directory is: > /cygdrive/c/MDProgram/Gromacs453/bin/molecule tests > I assume that .../Gromacs453/bin is the location where the Gromacs binaries are installed? It's a bad idea to run commands from the location of the installation or its subdirectories. It's also a possibility that the space in "molecule tests" is causing problems with filename parsing, but that's a bit of a guess. Move the necessary files to a new location, in a directory named without spaces, and try again. -Justin > --- On *Wed, 2/2/11, Justin A. Lemkul /<jalem...@vt.edu>/* wrote: > > > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] luck > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Wednesday, February 2, 2011, 2:15 AM > > > > Mr Bernard Ramos wrote: > > Hi! > > I am actually following your lysozyme tutorial. I ve been using > different pdb files including that of water, methanol, 1AKI, etc. > The pdb2gmx does not generate any topology file. No files are > generated and I get this error: > > ------------------------------------------ > > pdb2gmx, VERSION 4.5.3 > > Source code file: futil.c, line:491 > > File input/output > > 1AKI.pdb > > For more.... etc > > ------------------------------------------ > > > > Then this file doesn't exist in the working directory. What is the > command you're issuing (exact copy and paste from the terminal, > please)? What are the contents of the working directory? > > -Justin > > > > > --- On *Mon, 1/31/11, Mr Bernard Ramos /<bgrquan...@yahoo.com > <http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com>>/* > wrote: > > > > > > From: Mr Bernard Ramos <bgrquan...@yahoo.com > <http://us.mc527.mail.yahoo.com/mc/compose?to=bgrquan...@yahoo.com>> > > Subject: Re: [gmx-users] luck > > To: jalem...@vt.edu > <http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>, > "Discussion list for GROMACS users" > > <gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>> > > Date: Monday, January 31, 2011, 1:14 PM > > > > thanks. > > Here is the error i mentioned a while back with > using pdb2gmx: > > ---------------------------------------------------------- > > File input/output error: > > filename.pdb > > For more information, visit ............ > > ---------------------------------------------------------- > > thanks for the time > > > > --- On *Mon, 1/31/11, Justin A. Lemkul /<jalem...@vt.edu > <http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* wrote: > > > > > > From: Justin A. Lemkul <jalem...@vt.edu > <http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>> > > Subject: Re: [gmx-users] luck > > To: "Gromacs Users' List" <gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>> > > Date: Monday, January 31, 2011, 12:33 PM > > > > > > > > Mr Bernard Ramos wrote: > > > Do I need to type in g_luck instead? > > > > > > > Typing an email and waiting for a response takes far more > time > > and effort than simply trying it yourself ;) > > > > -Justin > > > > > --- On *Mon, 1/31/11, Justin A. Lemkul > /<jalem...@vt.edu > <http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>>/* > > wrote: > > > > > > > > > From: Justin A. Lemkul <jalem...@vt.edu > <http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=jalem...@vt.edu>> > > > Subject: Re: [gmx-users] luck > > > To: "Discussion list for GROMACS users" > > <gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>> > > > Date: Monday, January 31, 2011, 12:11 PM > > > > > > > > > > > > Mr Bernard Ramos wrote: > > > > Hi everyone! > > > > I have two questions. > > > > 1. after I installed gromacs 4.5.3 and "which > mdrun" > > was able to > > > give the correct path, I was not able to run "luck". > > Instead, "luck" > > > gives an error "command not found". Is this ok? > What went > > wrong? Do > > > I need to install again gromacs? > > > > > > > The program is now called g_luck. > > > > > > > 2. I tried doing "pdb2gmx". The error points the > > structure file > > > "*.pdb" as the error. Does this in dicate that the > > program was not > > > installed properly or there is an error with the > pdb file. > > > > > > > If the program has given you a fatal error, then the > > program is > > > correctly installed and working. It is your input > that > > is somehow > > > wrong. Without the actual error message, it's > impossible > > to say > > > what's wrong. > > > > > > -Justin > > > > > > > Thanks > > > > > > > > > > -- ======================================== > > > > > > Justin A. Lemkul > > > Ph.D. Candidate > > > ICTAS Doctoral Scholar > > > MILES-IGERT Trainee > > > Department of Biochemistry > > > Virginia Tech > > > Blacksburg, VA > > > jalemkul[at]vt.edu | (540) 231-9080 > > > >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > > > ======================================== > > > -- gmx-users mailing list gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/Search > > before posting! > > > Please don't post (un)subscribe requests to the > list. Use > > the www > > > interface or send it to > gmx-users-requ...@gromacs.org > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org> > > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > > > Can't post? Read > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > -- ======================================== > > > > Justin A. Lemkul > > Ph.D. Candidate > > ICTAS Doctoral Scholar > > MILES-IGERT Trainee > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > > ======================================== > > -- gmx-users mailing list gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search > before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > -----Inline Attachment Follows----- > > > > -- gmx-users mailing list gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org> > > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- gmx-users mailing list gmx-users@gromacs.org > <http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org > ><http://us.mc527.mail.yahoo.com/mc/compose?to=gmx-users-requ...@gromacs.org>. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
