Thank you very much, Mark! Now i have errors from my .top file after grompp command. The question is that why in pdb2gmx, editconf ,genbox and make_ndx steps i don't see these errors:
... processing topology... Opening library file /usr/share/gromacs/top/ffoplsaa.itp Opening library file /usr/share/gromacs/top/ffoplsaanb.itp Opening library file /usr/share/gromacs/top/ffoplsaabon.itp Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations ERROR 1 [file topol.top, line 412]: No default Angle types ERROR 2 [file topol.top, line 567]: No default Ryckaert-Bell. types ERROR 3 [file topol.top, line 570]: No default Ryckaert-Bell. types ERROR 4 [file topol.top, line 573]: No default Ryckaert-Bell. types ERROR 5 [file topol.top, line 580]: No default Ryckaert-Bell. types ERROR 6 [file topol.top, line 581]: No default Ryckaert-Bell. types ERROR 7 [file topol.top, line 582]: No default Ryckaert-Bell. types Opening library file /usr/share/gromacs/top/spc.itp Opening library file /usr/share/gromacs/top/ions.itp Excluding 3 bonded neighbours molecule type 'Protein' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 664]: System has non-zero total charge: 6.000000e-02 processing coordinates... double-checking input for internal consistency... renumbering atomtypes... converting bonded parameters... There was 1 note ------------------------------------------------------- Program grompp, VERSION 4.0.7 Source code file: ../../../../src/kernel/grompp.c, line: 986 Fatal error: There were 7 errors in input file(s) *topol.top:* ... 43 opls_238 3 BOC N 17 -0.5 14.0067 ; qtot 0.5 44 opls_241 3 BOC H 17 0.3 1.008 ; qtot 0.8 45 opls_283 3 BOC CA 17 0.04 12.011 ; qtot 0.84 46 opls_140 3 BOC HA1 17 0.06 1.008 ; qtot 0.9 47 opls_140 3 BOC HA2 17 0.06 1.008 ; qtot 0.96 48 opls_149 3 BOC CB 18 0.055 12.011 ; qtot 1.015 49 opls_140 3 BOC HB 18 0.06 1.008 ; qtot 1.075 50 opls_145 3 BOC CG1 18 -0.115 12.011 ; qtot 0.96 51 opls_145 3 BOC CD1 19 -0.115 12.011 ; qtot 0.845 52 opls_146 3 BOC HD1 19 0.115 1.008 ; qtot 0.96 53 opls_145 3 BOC CD2 20 -0.115 12.011 ; qtot 0.845 54 opls_146 3 BOC HD2 20 0.115 1.008 ; qtot 0.96 55 opls_145 3 BOC CE1 21 -0.115 12.011 ; qtot 0.845 56 opls_146 3 BOC HE1 21 0.115 1.008 ; qtot 0.96 57 opls_145 3 BOC CE2 22 -0.115 12.011 ; qtot 0.845 58 opls_146 3 BOC HE2 22 0.115 1.008 ; qtot 0.96 59 opls_145 3 BOC CZ 23 1 12.011 ; qtot 1.96 60 opls_264 3 BOC Cl 23 -1 35.453 ; qtot 0.96 61 opls_224B 3 BOC CG2 24 -0.12 12.011 ; qtot 0.84 62 opls_140 3 BOC HG1 24 0.06 1.008 ; qtot 0.9 63 opls_140 3 BOC HG2 24 0.06 1.008 ; qtot 0.96 64 opls_271 3 BOC C 25 0.7 12.011 ; qtot 1.66 65 opls_272 3 BOC O1 25 -0.8 15.9994 ; qtot 0.86 66 opls_272 3 BOC O2 25 -0.8 15.9994 ; qtot 0.06 ... [ angles ] ... line 412: 45 48 61 1 ... [ dihedrals ] ... line 567: 43 45 48 61 3 ... line 570: 46 45 48 61 3 ... line 573: 47 45 48 61 3 ... line 580: 45 48 61 62 3 line 581: 45 48 61 63 3 line 582: 45 48 61 64 3 ... it seems that "45 48 61" is the problem. CA CB CG2 Where i should define angle type for it?
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