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 ------------------------------------------
--- On Mon, 1/31/11, Mr Bernard Ramos <[email protected]> wrote: From: Mr Bernard Ramos <[email protected]> Subject: Re: [gmx-users] luck To: [email protected], "Discussion list for GROMACS users" <[email protected]> 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 <[email protected]> wrote: From: Justin A. Lemkul <[email protected]> Subject: Re: [gmx-users] luck To: "Gromacs Users' List" <[email protected]> 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 /<[email protected]>/* wrote: > > > From: Justin A. Lemkul <[email protected]> > Subject: Re: [gmx-users] luck > To: "Discussion list for GROMACS users" <[email protected]> > 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 [email protected] > <http://us.mc527.mail.yahoo.com/mc/[email protected]> > 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 [email protected] > ><http://us.mc527.mail.yahoo.com/mc/[email protected]>. > 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 [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -----Inline Attachment Follows----- -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
