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
--- 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>/* wrote: > > > From: Mr Bernard Ramos <bgrquan...@yahoo.com> > Subject: Re: [gmx-users] luck > To: jalem...@vt.edu, "Discussion list for GROMACS users" > <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>/* wrote: > > > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] luck > To: "Gromacs Users' List" <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>>/* > 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: "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, 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://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 > > > > -----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://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
