Dear Gromacs Users, I have performed the Martini Coarse Graining procedure for the simulation of two protein domains by using the two scripts atom2cg.awk and seq2itp.pl. Then I was able to perform my simulation of my coarse grained system. My problem is now to convert my final cg structure into an all atom structure. For this purpose I tried to use the tool g_fg2cg with the inputs containing my fine grained topology ,the coarse grained topology and my coarse grained structure file. But obviously all attempts to apply that tool ended up in a segmentation fault message. I also tried to convert my all atom structure into a cg structure which ended up with the same segmentation fault message. Could you give me some advice on that problem? Here is my screen output: Option Filename Type Description ------------------------------------------------------------ -pfg LOV1_LOV2.pdb.top Input Topology file -pcg martini_v2.0_example.top Input, Opt! Topology file -c lov1lov2_42ns_27.1.pdb Input Generic trajectory: xtc trr trj gro g96 pdb -o out.gro Output Generic structure: gro g96 pdb xml
Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -n int 0 1: fg2cg transformation, 0: cg2fg transformation -wat int 0 1: rewrites FG_CG water to true fg water; -rad real 0.3 A radius for random atom insertion; calling cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 3 bonded neighbours for Protein_B 1 NOTE: System has non-zero total charge: -2.999998e+00 # G96BONDS: 2738 # G96ANGLES: 3994 # PDIHS: 1465 # IDIHS: 1328 # LJ14: 4520 calling cpp... processing topology... Generated 0 of the 465 non-bonded parameter combinations Excluding 1 bonded neighbours for Protein 1 Excluding 1 bonded neighbours for ProteinB 1 NOTE: System has non-zero total charge: -6.000000e+00 Number of fg atoms 2696 Number of cg atoms 571 Reading frame 0 time 42000.004 1264673691 Segmentation fault When I applied this tool on the ubiquitin example I had another problem, but I did it in the same way as before. Here is the screen output: Option Filename Type Description ------------------------------------------------------------ -pfg 1ubq.top Input Topology file -pcg out3.top Input, Opt! Topology file -c 1UBQ.gro Input Generic trajectory: xtc trr trj gro g96 pdb -o out.gro Output Generic structure: gro g96 pdb xml Option Type Value Description ------------------------------------------------------ -[no]h bool no Print help info and quit -nice int 0 Set the nicelevel -n int 1 1: fg2cg transformation, 0: cg2fg transformation -wat int 0 1: rewrites FG_CG water to true fg water; -rad real 0.3 A radius for random atom insertion; calling cpp... processing topology... Generated 279 of the 1225 non-bonded parameter combinations Excluding 3 bonded neighbours for Protein_A 1 Excluding 2 bonded neighbours for SOL 58 # G96BONDS: 766 # G96ANGLES: 1107 # PDIHS: 428 # IDIHS: 334 # LJ14: 1304 # SETTLE: 58 calling cpp... cpp: out3.top: Datei oder Verzeichnis nicht gefunden cpp: warning: '-x c' after last input file has no effect cpp: no input files cpp exit code: 256 Tried to execute: 'cpp -I/pc50417/pee18323/REVERSE_trans_gromacs/agromacs-reverse/share/top out3.top > grompp605Sk3' The 'cpp' command is defined in the .mdp file processing topology... Number of fg atoms 934 Number of cg atoms 0 Reading frames from gro file 'UBIQUITIN', 934 atoms. Reading frame 0 time 0.000 out.xtc Last frame 0 time 0.000 Back Off! I just backed up out.gro to ./#out.gro.2# Cg structure computed ! In that case out.gro did not contain any atoms. Thanks for any suggestions! Best regards, Emanuel Peter -- 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/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/mailing_lists/users.php