HI Justin, I did use the .pdb file as I showed in the grompp command. If I got I/O error, the mdrun should not work? but here the mdrun is working. Thanks.
On Wed, Jun 13, 2012 at 9:14 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 6/13/12 9:11 AM, Malai wrote: > >> Hello Justin, >> >> Thanks for reply. After getting this, I started to run production run but >> here i >> didnt get any error. so is it OK? or still I need to look at this error? >> Thanks >> >> > What's anomalous to me is that grompp produced an I/O error (referencing > an unused or nonexistent file) but still produced a .tpr file. Fatal > errors prevent grompp from working, so you shouldn't have gotten a .tpr > file in this case. > > You need coordinates in the .tpr file to work, but if you did in fact use > a .pdb file, then the .tpr is fine. The reference to the .gro file is > still a complete mystery to me. > > -Justin > > On Wed, Jun 13, 2012 at 8:35 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@vt.edu>> wrote: >> >> >> >> On 6/13/12 8:27 AM, Malai wrote: >> >> HI, >> >> Sorry for wrongly typing. The command I issued is: grompp -v -f >> hex1.mdp -c >> hex1.pdb -p hex1.top -o hex1.tpr. >> >> The error is bellow: >> >> >> Error: >> Program grompp, VERSION 4.5.4 >> Source code file: futil.c, line: 491 >> >> File input/output error: >> hex1.gro >> For more information and tips for troubleshooting, please check >> the GROMACS >> website at >> http://www.gromacs.org/____**Documentation/Errors<http://www.gromacs.org/____Documentation/Errors> >> >> <http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors> >> > >> >> >> <http://www.gromacs.org/__**Documentation/Errors<http://www.gromacs.org/__Documentation/Errors> >> >> <http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> >> >> >> >> Even with the corrected command, I see no way for this error to come >> up. >> There is no reference to a .gro file anywhere in your command. >> >> >> -Justin >> >> -- >> ==============================**__========== >> >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) >> 231-9080<tel:%28540%29%20231-9080> >> >> http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin> >> >> <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> >> > >> >> ==============================**__========== >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org <mailto: >> gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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