I read about .hdb file and then i editted my .hdb file: ... BOC 9 1 1 H N -C CA 2 6 HA CA N CB 1 5 HB CB CA CG1 CG2 1 1 HD1 CD1 CG1 CE1 1 1 HD2 CD2 CG1 CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 2 6 HG CG2 CB C CYS2 3 1 1 H N -C CA 1 5 HA CA N C CB 2 6 HB CB SG CA ... PHE 8 1 1 H N -C CA 1 5 HA CA N C CB 2 6 HB CB CG CA 1 1 HD1 CD1 CG CE1 1 1 HD2 CD2 CG CE2 1 1 HE1 CE1 CD1 CZ 1 1 HE2 CE2 CD2 CZ 1 1 HZ CZ CE1 CE2 ...
but i got this error: ... There are 1 chains and 0 blocks of water and 3 residues with 63 atoms chain #res #atoms 1 ' ' 3 63 All occupancy fields zero. This is probably not an X-Ray structure Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 1 Reading residue database... (ffoplsaa) Opening library file /usr/share/gromacs/top/ffoplsaa.rtp Residue 57 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb ------------------------------------------------------- Program pdb2gmx, VERSION 4.0.7 Source code file: ../../../../src/kernel/h_db.c, line: 87 Fatal error: wrong format in input file ffoplsaa.hdb on line CYS2 3
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