oh!!!!..no i mean that instead of.pdb file i used .gro file..from the begining...in the tutorial they dont change to .gro type.. but i do...and i carefully apply....i am able to run mdrun command for energy minimisation..and in this command i want output file ..so i used *-c fws_b4pr.gro*...but when i ran grompp for position restrained it show the error..though the file has been created in directory/server
On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul <[email protected]> wrote: > > > mohit kumar wrote: > >> im trying this spider toxin tutorial as beginner ....the mdrun command >> after energy minimization have *-c fws_b4pr.pdb(i make .gro)* and then on >> page no 9 the grompp command for the postion restrained uses *-c >> fws_b4pr.gro* and when i run it show: >> Program grompp, VERSION 4.0.2 >> Source code file: futil.c, line: 330 >> >> File input/output error: >> fws_b4pr.gro >> ------------------------------ >> ------------------------- >> >> "Hey Man You Know, I'm Really OK" (Offspring) >> what may be the reason for this..im really confused!!! >> >> > Probably a typo or you lack read/write permissions in the directory. > Otherwise, how did you "make .gro?" Did you use editconf, or did you just > rename the file? > > -Justin > > >> -- >> MOHIT KUMAR >> Molecular Biochemistry & Biophysics >> Graduate Student >> Illinois Institute of Technology >> Chicago,IL, USA >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> 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 | (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/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/mailing_lists/users.php > -- MOHIT KUMAR Molecular Biochemistry & Biophysics Graduate Student Illinois Institute of Technology Chicago,IL, USA
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