Hi, I deleted the old one and moved another one using box.com since scp doesn't work, but I got the same results. Any ideas?
/Elsaid On Tue, Nov 10, 2015 at 3:02 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 11/9/15 7:59 PM, Elsaid Younes wrote: > >> Hi, >> >> it gives me file input/output error 1aki.pdb. >> >> > The most likely explanation is that file doesn't exist in the working > directory. > > -Justin > > > 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 What appears here is a (very) outdated version of GROMACS, and 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. >>>> >>>> >>> >>> > -- > ================================================== > > 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.