I tried to use the command pdb2gmx *kumud@ubuntu:~/gromacs/gromacs-4.5.5/share/tutor/mciz$ pdb2gmx -ignh -ff G43a1 -f mciz.pdb -o mciz.gro -p mciz.top*
At the end the message came as *Program pdb2gmx, VERSION 4.5.5 Source code file: pdb2top.c, line: 239 Fatal error: Could not find force field 'G43a1' in current directory, install tree or GMXDATA path.* What is the problem here? Thanks Kumud Agarwal On Tue, Jan 24, 2012 at 9:38 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > kumud agarwal wrote: > >> How can I check if Gromacs is properly installed on my system (ubuntu)? >> >> > http://www.gromacs.org/**Downloads/Installation_** > Instructions#Getting_access_**to_GROMACS_after_installation<http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation> > > Then try any of the commands. > > -Justin > > On Tue, Jan 24, 2012 at 9:22 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> kumud agarwal wrote: >> >> hi >> >> I am very new to Gromacs. >> >> To start working with Gromacs in which directory do I have to >> keep the pdb file that I am working on? >> >> >> You put files in whichever directory you want to do your work >> (provided you have sufficient permission to write in that directory). >> >> -Justin >> >> -- ==============================**__========== >> >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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<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. 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<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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