ok.thanx very much .......so but it happens generally to all tutorials i have done..means...grompp not able to find .gro files....i have tried 3-4 tutorial..and i stuck at same place everytime. please tell me how to download coordinate files... thnx again..for your help!!
On Sun, Jul 12, 2009 at 9:01 PM, Justin A. Lemkul <[email protected]> wrote: > > > mohit kumar wrote: > >> i write down all steps till i got stuck...my server is using 4.0.2 >> version..ya fws_b4pr.gro is successfully created..someone suggest me its may >> be due to excessive charge...i dnt get that point. >> >> > I don't understand what "excessive charge" would be about. All the > commands work perfectly on my local machine, therefore, they should work. I > would be willing to bet that you're seeing a filesystem blip and grompp > can't find your coordinate file (either momentarily or ever). Again, I > recommend downloading the coordinate file and processing with grompp on a > local machine. > > -Justin > > On Sun, Jul 12, 2009 at 8:16 PM, Justin A. Lemkul <[email protected]<mailto: >> [email protected]>> wrote: >> >> >> >> mohit kumar wrote: >> >> 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 >> >> >> So fws_b4pr.gro was successfully created, but then grompp can't find >> it? Maybe you're seeing some sort of network/NFS problem when >> accessing the server. Do you have a local machine where you can try >> again? Otherwise, post all your commands exactly as you have >> entered them to see if anyone can spot a typo or other problem. >> >> -Justin >> >> On Sun, Jul 12, 2009 at 7:47 PM, Justin A. Lemkul >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[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] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[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 <http://vt.edu> <http://vt.edu> | (540) >> 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[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 >> >> >> -- ======================================== >> >> 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 [email protected] >> <mailto:[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] >> <mailto:[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 >> >> > -- > ======================================== > > 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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