Dear all, I have tried to process the heme containing protein using GROMOS 54a7. Although I am able to convert the pro.pdb to pro.gro, I am getting a warning sign, like this, -------------------------------------- While running pdb2gmx -f pro.pdb -o pro.gro .... . . . Before cleaning: 9225 pairs Before cleaning: 11318 dihedrals Making cmap torsions... There are 3062 dihedrals, 3024 impropers, 8613 angles 9225 pairs, 5884 bonds and 0 virtual sites Total mass 63413.819 a.m.u. Total charge -1.000 e Writing topology Processing chain 2 'A' (43 atoms, 1 residues) Warning: Starting residue HEM605 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Special Atom Distance matrix: HEM605 HEM605 CAB20 CAC27 HEM605 CAC27 0.815 HEM605 Fe43 0.582 0.570 Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 1 residues with 47 atoms Chain time... Making bonds... Number of bonds was 54, now 54 Generating angles, dihedrals and pairs... Before cleaning: 15 pairs Before cleaning: 154 dihedrals Making cmap torsions... There are 20 dihedrals, 46 impropers, 102 angles 15 pairs, 54 bonds and 0 virtual sites Total mass 614.485 a.m.u. Total charge -2.000 e Writing topology Including chain 1 in system: 5752 atoms 552 residues Including chain 2 in system: 47 atoms 1 residues Now there are 5799 atoms and 553 residues Total mass in system 64028.304 a.m.u. Total charge in system -3.000 e ----------------------------------------------------------------- And when I try to add ions using grompp and ions.mdp i get this... NOTE 1 [file ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.
Setting the LD random seed to 1795342617 Generated 279 of the 1225 non-bonded parameter combinations ERROR 1 [file topol_Other_chain_A2.itp, line 162]: No default G96Angle types ERROR 2 [file topol_Other_chain_A2.itp, line 164]: No default G96Angle types ERROR 3 [file topol_Other_chain_A2.itp, line 167]: No default G96Angle types ERROR 4 [file topol_Other_chain_A2.itp, line 169]: No default G96Angle types ERROR 5 [file topol_Other_chain_A2.itp, line 172]: No default G96Angle types ERROR 6 [file topol_Other_chain_A2.itp, line 174]: No default G96Angle types ERROR 7 [file topol_Other_chain_A2.itp, line 177]: No default G96Angle types ERROR 8 [file topol_Other_chain_A2.itp, line 179]: No default G96Angle types -------------------------- Could you please suggest a solution. Would it help, if i added the following line to residues.dat in $gmx$ --- . . IB+ Ion HEM Protein -- Regards, Prasanth. -- 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.