im using dell core 2 duo with linux mint On Mon, Aug 10, 2009 at 10:37 AM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > mohit kumar wrote: > >> still im getting problem, i checked the funct its have numerical >> value..stilll getting problem..do i have to install gromac 3 version for >> that..coz i having 4.0.5 version... >> >> > Working with the most recent version (4.0.5) is always recommended. The > only reason to use an old version would be for consistency with older work. > Can you post your [ pairs ] section so we can have a look? What type of > machine are you using? If it's Windows, then there may be problems with the > file if it was edited using anything other than a plain text editor, in > which case dos2unix is your friend. > > -Justin > > On Thu, Aug 6, 2009 at 3:22 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> mohit kumar wrote: >> >> but i dnt find any 'type' column in my topology file..the grompp >> programm with this top file works gud in 3.3 version..im having >> 4.0.5 version..is that can be issue?? shud i try in 3.3 version >> >> >> This may be some new error-checking mechanism introduced in version >> 4.0. In your topology, a function type for pairs should be defined, >> according to the header of this section (from pdb2gmx): >> >> [ pairs ] >> ; ai aj funct c0 c1 c2 >> c3 >> >> If your "funct" column is blank or says "0" then that could be >> giving the error. >> >> -Justin >> >> On Thu, Aug 6, 2009 at 2:48 PM, Justin A. Lemkul >> <jalem...@vt.edu <mailto:jalem...@vt.edu> >> <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote: >> >> >> >> mohit kumar wrote: >> >> im running energy minimization for POPC bilayer but its >> showing >> error which i cant figure out >> >> -- ------------------------------------------------------- >> Program grompp, VERSION 4.0.5 >> Source code file: topdirs.c, line: 99 >> >> Fatal error: >> Invalid pairs type 0 >> >> what does this pair type mean and how can i solve it?? >> plz help me >> >> >> The error message is pretty clear. Somewhere within the >> topology, >> you have a "0" in the "type" column, which doesn't correspond >> to any >> known pair type. >> >> -Justin >> >> >> >> MOHIT KUMAR >> Molecular Biochemistry & Biophysics >> Graduate Student >> Illinois Institute of Technology >> Chicago,IL, USA >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org >> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read >> http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> <mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> 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-requ...@gromacs.org> >> <mailto:gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- MOHIT KUMAR >> Molecular Biochemistry & Biophysics >> Graduate Student >> Illinois Institute of Technology >> Chicago,IL, USA >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> 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 >> Please search the archive at http://www.gromacs.org/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-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> MOHIT KUMAR >> Molecular Biochemistry & Biophysics >> Graduate Student >> Illinois Institute of Technology >> Chicago,IL, USA >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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/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/mailing_lists/users.php > -- MOHIT KUMAR Molecular Biochemistry & Biophysics Graduate Student Illinois Institute of Technology Chicago,IL, USA
popc_43A1-S3.itp
Description: Binary data
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