Hi, it gives me file input/output error 1aki.pdb.
Elsaid On Mon, Nov 9, 2015 at 8:20 PM, Elsaid Younes <elk...@gmail.com> wrote: > Thank you! > > On Mon, Nov 9, 2015 at 8:18 PM, Samuel Flores <samuelflor...@gmail.com> > wrote: > >> Oh that makes sense! >> >> Elsaid, issue: >> >> module load gromacs/5.0.4 >> >> "module load gromacs" defaults to an ancient release of gromacs. >> >> Sam >> >> > On Nov 9, 2015, at 19:10, Justin Lemkul <jalem...@vt.edu> wrote: >> > >> > >> > >> > On 11/9/15 1:08 PM, Samuel Flores wrote: >> >> Hi Justin, >> >> >> >> Is gmx the same as ngmx? Here are the binaries in the Uppmax gromacs >> directory: >> >> >> > >> > gmx refers to the single binary provided as of 5.0, which is the new >> setup. What appears here is a (very) outdated version of GROMACS, and usage >> needs to be adjusted accordingly. >> > >> > -Justin >> > >> >> [samuelf@tintin1 ~]$ ls /sw/apps/gromacs/4.6.3/tintin/bin/ >> >> GMXRC g_anadock_d g_cluster g_densorder_d >> g_enemat g_helixorient_d g_morph g_pme_error_d g_rmsdist >> g_select_d g_traj genbox make_edi_d trjcat_d >> >> GMXRC.bash g_anaeig g_cluster_d g_dielectric g_enemat_d >> g_hydorder g_morph_d g_polystat g_rmsdist_d g_sgangle >> g_traj_d genbox_d make_ndx trjconv >> >> GMXRC.csh g_anaeig_d g_clustsize g_dielectric_d g_energy >> g_hydorder_d g_msd g_polystat_d g_rmsf g_sgangle_d >> g_tune_pme genconf make_ndx_d trjconv_d >> >> GMXRC.zsh g_analyze g_clustsize_d g_dipoles g_energy_d >> g_kinetics g_msd_d g_potential g_rmsf_d g_sham >> g_tune_pme_d genconf_d mdrun trjorder >> >> completion.bash g_analyze_d g_confrms g_dipoles_d g_filter >> g_kinetics_d g_nmeig g_potential_d g_rotacf >> g_sham_d g_vanhove genion mdrun_d trjorder_d >> >> completion.csh g_angle g_confrms_d g_disre >> g_filter_d g_lie g_nmeig_d g_principal g_rotacf_d >> g_sigeps g_vanhove_d genion_d mdrun_mpi xplor2gmx.pl >> >> completion.zsh g_angle_d g_covar g_disre_d >> g_gyrate g_lie_d g_nmens g_principal_d g_rotmat >> g_sigeps_d g_velacc genrestr mdrun_mpi_d xplor2gmx.pl~ >> >> demux.pl g_bar g_covar_d g_dist g_gyrate_d >> g_luck g_nmens_d g_protonate g_rotmat_d g_sorient >> g_velacc_d genrestr_d mk_angndx xpm2ps >> >> do_dssp g_bar_d g_current g_dist_d >> g_h2order g_luck_d g_nmtraj g_protonate_d g_saltbr >> g_sorient_d g_wham gmxcheck mk_angndx_d xpm2ps_d >> >> do_dssp_d g_bond g_current_d g_dos g_h2order_d >> g_mdmat g_nmtraj_d g_rama g_saltbr_d g_spatial >> g_wham_d gmxcheck_d ngmx >> >> editconf g_bond_d g_density g_dos_d g_hbond >> g_mdmat_d g_options g_rama_d g_sans g_spatial_d >> g_wheel gmxdump pdb2gmx >> >> editconf_d g_bundle g_density_d g_dyecoupl g_hbond_d >> g_membed g_options_d g_rdf g_sans_d g_spol >> g_wheel_d gmxdump_d pdb2gmx_d >> >> eneconv g_bundle_d g_densmap g_dyecoupl_d >> g_helix g_membed_d g_order g_rdf_d g_sas >> g_spol_d g_x2top grompp tpbconv >> >> eneconv_d g_chi g_densmap_d g_dyndom g_helix_d >> g_mindist g_order_d g_rms g_sas_d g_tcaf >> g_x2top_d grompp_d tpbconv_d >> >> g_anadock g_chi_d g_densorder g_dyndom_d >> g_helixorient g_mindist_d g_pme_error g_rms_d g_select >> g_tcaf_d g_xrama make_edi trjcat >> >> >> >> >> >> Elsaid, >> >> >> >> Regarding Justin’s suggestion, on Uppmax I believe the full path would >> be: >> >> >> >> source /sw/apps/gromacs/4.6.3/tintin/bin/GMXRC.bash >> >> >> >> >> >> However I think you already issued >> >> >> >> module load gromacs >> >> >> >> which might source GMXRC . >> >> >> >> Sam >> >> >> >> >> >>> On Nov 9, 2015, at 17:56, Justin Lemkul <jalem...@vt.edu> wrote: >> >>> >> >>> >> >>> >> >>> On 11/9/15 11:55 AM, Elsaid Younes wrote: >> >>>> Hi, >> >>>> >> >>>> Thank you for your response. >> >>>> When writing gmx, it gives the command not found. (Note I use >> windows) >> >>>> >> >>> >> >>> Then you haven't configured your environment correctly. >> >>> >> >>> >> http://www.gromacs.org/Documentation/Installation_Instructions_5.0#getting-access-to-gromacs-after-installation >> >>> >> >>> -Justin >> >>> >> >>> -- >> >>> ================================================== >> >>> >> >>> Justin A. Lemkul, Ph.D. >> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >>> >> >>> Department of Pharmaceutical Sciences >> >>> School of Pharmacy >> >>> Health Sciences Facility II, Room 629 >> >>> University of Maryland, Baltimore >> >>> 20 Penn St. >> >>> Baltimore, MD 21201 >> >>> >> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> >>> http://mackerell.umaryland.edu/~jalemkul >> >>> >> >>> ================================================== >> >>> -- >> >>> Gromacs Users mailing list >> >>> >> >>> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >>> >> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >>> >> >>> * For (un)subscribe requests visit >> >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users >> or send a mail to gmx-users-requ...@gromacs.org. >> >> >> > >> > -- >> > ================================================== >> > >> > Justin A. Lemkul, Ph.D. >> > Ruth L. Kirschstein NRSA Postdoctoral Fellow >> > >> > Department of Pharmaceutical Sciences >> > School of Pharmacy >> > Health Sciences Facility II, Room 629 >> > University of Maryland, Baltimore >> > 20 Penn St. >> > Baltimore, MD 21201 >> > >> > jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> > http://mackerell.umaryland.edu/~jalemkul >> > >> > ================================================== >> > -- >> > Gromacs Users mailing list >> > >> > * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >> > * For (un)subscribe requests visit >> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.