Dear all, I have got an analysis tool for analyzing membrane density from Dr.Luca monticelli. I have followed the installation instructions as given.
1) First thing is to load GROMACS $ *source /usr/local/gromacs/bin/GMXRC* 2) Enter the source directory of the program then make $ cd g_mydensity $ make According to the instructions, it should create an executable "*g_mydensity*" but I am getting the following errors *cc `pkg-config --libs libgmx` g_mydensity.o matrix.o distances.o dist_mode.o grid_mode.o -o g_mydensity* *g_mydensity.o: In function `gmx_log2':* *g_mydensity.c:(.text+0xa8): undefined reference to `log'* *g_mydensity.o: In function `gmx_invsqrt':* *g_mydensity.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* *g_mydensity.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'* *g_mydensity.o: In function `matrix_convert':* *g_mydensity.c:(.text+0x381): undefined reference to `cos'* *g_mydensity.c:(.text+0x3ad): undefined reference to `sin'* *g_mydensity.c:(.text+0x3da): undefined reference to `cos'* *g_mydensity.c:(.text+0x403): undefined reference to `cos'* *g_mydensity.c:(.text+0x416): undefined reference to `cos'* *g_mydensity.c:(.text+0x429): undefined reference to `cos'* *g_mydensity.c:(.text+0x447): undefined reference to `sin'* *g_mydensity.c:(.text+0x4ad): undefined reference to `sqrt'* *g_mydensity.o: In function `get_electrons':* *g_mydensity.c:(.text+0x527): undefined reference to `ffopen'* *g_mydensity.c:(.text+0x564): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x5b6): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x600): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x62e): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x68d): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x6eb): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x74f): undefined reference to `ffclose'* *g_mydensity.o: In function `center_coords':* *g_mydensity.c:(.text+0x88f): undefined reference to `calc_box_center'* *g_mydensity.o: In function `calc_electron_density':* *g_mydensity.c:(.text+0x945): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x973): undefined reference to `read_first_x'* *g_mydensity.c:(.text+0x9a0): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0xa38): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0xa81): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0xac1): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0xaf6): undefined reference to `gmx_rmpbc_init'* *g_mydensity.c:(.text+0xb18): undefined reference to `set_pbc'* *g_mydensity.c:(.text+0xb38): undefined reference to `gmx_rmpbc'* *g_mydensity.c:(.text+0xe0b): undefined reference to `read_next_x'* *g_mydensity.c:(.text+0xe1e): undefined reference to `gmx_rmpbc_done'* *g_mydensity.c:(.text+0xe29): undefined reference to `close_trj'* *g_mydensity.c:(.text+0xecc): undefined reference to `save_free'* *g_mydensity.o: In function `calc_density':* *g_mydensity.c:(.text+0xf32): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0xf60): undefined reference to `read_first_x'* *g_mydensity.c:(.text+0xf8d): undefined reference to `gmx_fatal'* *g_mydensity.c:(.text+0x101c): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x1065): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x10a5): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x10da): undefined reference to `gmx_rmpbc_init'* *g_mydensity.c:(.text+0x10fc): undefined reference to `set_pbc'* *g_mydensity.c:(.text+0x111c): undefined reference to `gmx_rmpbc'* *g_mydensity.c:(.text+0x143a): undefined reference to `read_next_x'* *g_mydensity.c:(.text+0x144d): undefined reference to `gmx_rmpbc_done'* *g_mydensity.c:(.text+0x146e): undefined reference to `close_trj'* *g_mydensity.c:(.text+0x1511): undefined reference to `save_free'* *g_mydensity.o: In function `plot_density':* *g_mydensity.c:(.text+0x159c): undefined reference to `xvgropen'* *g_mydensity.c:(.text+0x15bf): undefined reference to `xvgr_legend'* *g_mydensity.c:(.text+0x16ea): undefined reference to `ffclose'* *g_mydensity.o: In function `gmx_mydensity':* *g_mydensity.c:(.text+0x18bd): undefined reference to `CopyRight'* *g_mydensity.c:(.text+0x1923): undefined reference to `parse_common_args'* *g_mydensity.c:(.text+0x19a0): undefined reference to `ftp2fn'* *g_mydensity.c:(.text+0x19af): undefined reference to `read_top'* *g_mydensity.c:(.text+0x1a84): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x1ab4): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x1ae4): undefined reference to `save_calloc'* *g_mydensity.c:(.text+0x1b0b): undefined reference to `ftp2fn_null'* *g_mydensity.c:(.text+0x1b39): undefined reference to `get_index'* *g_mydensity.c:(.text+0x1b67): undefined reference to `ftp2fn'* *g_mydensity.c:(.text+0x1be1): undefined reference to `ftp2fn'* *g_mydensity.c:(.text+0x1c6a): undefined reference to `opt2fn_null'* *g_mydensity.c:(.text+0x1caa): undefined reference to `opt2fn'* *g_mydensity.c:(.text+0x1d04): undefined reference to `opt2bSet'* *g_mydensity.c:(.text+0x1d36): undefined reference to `ftp2fn'* *g_mydensity.c:(.text+0x1d63): undefined reference to `opt2fn'* *g_mydensity.c:(.text+0x1e20): undefined reference to `ftp2fn'* *g_mydensity.c:(.text+0x1edb): undefined reference to `opt2fn'* *g_mydensity.c:(.text+0x1f39): undefined reference to `opt2fn'* *g_mydensity.c:(.text+0x1f50): undefined reference to `do_view'* *g_mydensity.c:(.text+0x1f5d): undefined reference to `thanx'* *matrix.o: In function `realMatrix':* *matrix.c:(.text+0x29): undefined reference to `save_malloc'* *matrix.c:(.text+0x66): undefined reference to `save_malloc'* *matrix.o: In function `deleteRealMat':* *matrix.c:(.text+0xe4): undefined reference to `save_free'* *matrix.c:(.text+0x113): undefined reference to `save_free'* *matrix.o: In function `intMatrix':* *matrix.c:(.text+0x142): undefined reference to `save_malloc'* *matrix.c:(.text+0x17f): undefined reference to `save_malloc'* *matrix.o: In function `deleteIntMat':* *matrix.c:(.text+0x1fd): undefined reference to `save_free'* *matrix.c:(.text+0x22c): undefined reference to `save_free'* *distances.o: In function `gmx_log2':* *distances.c:(.text+0xa8): undefined reference to `log'* *distances.o: In function `gmx_invsqrt':* *distances.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* *distances.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'* *distances.o: In function `matrix_convert':* *distances.c:(.text+0x332): undefined reference to `cos'* *distances.c:(.text+0x35e): undefined reference to `sin'* *distances.c:(.text+0x38b): undefined reference to `cos'* *distances.c:(.text+0x3b4): undefined reference to `cos'* *distances.c:(.text+0x3c7): undefined reference to `cos'* *distances.c:(.text+0x3da): undefined reference to `cos'* *distances.c:(.text+0x3f8): undefined reference to `sin'* *distances.c:(.text+0x45e): undefined reference to `sqrt'* *distances.o: In function `pbc_rvec_sub':* *distances.c:(.text+0x4e8): undefined reference to `pbc_dx'* *distances.o: In function `get_distance':* *distances.c:(.text+0x550): undefined reference to `sqrtf'* *distances.o: In function `center_of_mass':* *distances.c:(.text+0x6b5): undefined reference to `save_calloc'* *dist_mode.o: In function `gmx_log2':* *dist_mode.c:(.text+0xa8): undefined reference to `log'* *dist_mode.o: In function `gmx_invsqrt':* *dist_mode.c:(.text+0xf2): undefined reference to `gmx_invsqrt_exptab'* *dist_mode.c:(.text+0x101): undefined reference to `gmx_invsqrt_fracttab'* *dist_mode.o: In function `norm':* *dist_mode.c:(.text+0x1fc): undefined reference to `sqrt'* *dist_mode.o: In function `matrix_convert':* *dist_mode.c:(.text+0x2fa): undefined reference to `cos'* *dist_mode.c:(.text+0x326): undefined reference to `sin'* *dist_mode.c:(.text+0x353): undefined reference to `cos'* *dist_mode.c:(.text+0x37c): undefined reference to `cos'* *dist_mode.c:(.text+0x38f): undefined reference to `cos'* *dist_mode.c:(.text+0x3a2): undefined reference to `cos'* *dist_mode.c:(.text+0x3c0): undefined reference to `sin'* *dist_mode.c:(.text+0x414): undefined reference to `sqrt'* *dist_mode.o: In function `_min_distance':* *dist_mode.c:(.text+0x505): undefined reference to `pbc_dx'* *dist_mode.o: In function `build_dist':* *dist_mode.c:(.text+0x5af): undefined reference to `save_calloc'* *dist_mode.c:(.text+0x65c): undefined reference to `save_calloc'* *dist_mode.c:(.text+0x6a3): undefined reference to `save_calloc'* *dist_mode.c:(.text+0x710): undefined reference to `save_calloc'* *dist_mode.c:(.text+0x73f): undefined reference to `save_calloc'* *dist_mode.o:dist_mode.c:(.text+0x76e): more undefined references to `save_calloc' follow* *dist_mode.o: In function `build_dist':* *dist_mode.c:(.text+0x7b2): undefined reference to `get_index'* *dist_mode.c:(.text+0x839): undefined reference to `xvgropen'* *dist_mode.c:(.text+0x865): undefined reference to `xvgr_legend'* *dist_mode.o: In function `clean_dist':* *dist_mode.c:(.text+0x8bd): undefined reference to `save_free'* *dist_mode.c:(.text+0x8f1): undefined reference to `save_free'* *dist_mode.c:(.text+0x917): undefined reference to `save_free'* *dist_mode.c:(.text+0x948): undefined reference to `save_free'* *grid_mode.o: In function `build_grids':* *grid_mode.c:(.text+0x81): undefined reference to `save_calloc'* *grid_mode.c:(.text+0x177): undefined reference to `gmx_fatal'* *grid_mode.c:(.text+0x1a2): undefined reference to `save_calloc'* *grid_mode.c:(.text+0x201): undefined reference to `ffopen'* *grid_mode.o: In function `clean_grids':* *grid_mode.c:(.text+0x2b8): undefined reference to `save_free'* *grid_mode.c:(.text+0x2c6): undefined reference to `ffclose'* *grid_mode.c:(.text+0x2e9): undefined reference to `save_free'* *grid_mode.o: In function `grid_store':* *grid_mode.c:(.text+0x41a): undefined reference to `put_atom_in_box'* *collect2: ld returned 1 exit status* *make: *** [g_mydensity] Error 1* Please help me in this regard. Thanks for your valuable time and concern. -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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