Hi all, There is an unnatural sidechain in my input file, so I added new lines as new-defined(DPP) residue to the .rtp and .hdb files. Also there were some missed bonds, angles, and dihedrals in generated .top file, which manually added in. When I go through the grompp to do EM, I find a fatal error about the new defined residue:
No default U-B types As I checked this kind of angle, it exists in other residues such as lysine as well. This angle is (defined by atom types): CT1 CT2 NH3 I checked the atom names, It seems ok. Part of the top file is as follow: residue 1 DPP rtp DPP q +2.0 1 NH3 1 DPP N 1 -0.3 14.007 ; qtot -0.3 2 HC 1 DPP H1 2 0.33 1.008 ; qtot 0.03 3 HC 1 DPP H2 3 0.33 1.008 ; qtot 0.36 4 HC 1 DPP H3 4 0.33 1.008 ; qtot 0.69 5 CT1 1 DPP CA 5 0.21 12.011 ; qtot 0.9 6 HB 1 DPP HA 6 0.1 1.008 ; qtot 1 7 CT2 1 DPP CB 7 0.21 12.011 ; qtot 1.21 8 HA 1 DPP HB1 8 0.05 1.008 ; qtot 1.26 9 HA 1 DPP HB2 9 0.05 1.008 ; qtot 1.31 10 NH3 1 DPP NG 10 -0.3 14.007 ; qtot 1.01 11 HC 1 DPP HG1 11 0.33 1.008 ; qtot 1.34 12 HC 1 DPP HG2 12 0.33 1.008 ; qtot 1.67 13 HC 1 DPP HG3 13 0.33 1.008 ; qtot 2 14 C 1 DPP C 14 0.51 12.011 ; qtot 2.51 15 O 1 DPP O 15 -0.51 15.999 ; qtot 2 Fatal error: ERROR 1 [file topol.top, line 853]: No default U-B types line 853: 5 7 10 5 Would you please let me your suggestions about the reason of this error? How can I pass it? Would you please help me? Thanks in advance for your suggestions. Sincerely, Shima -- 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.
