Hello, My protein is pr-DNA complex, it is identifying DNA terminus and searching for N and C in tdb file giving error. When I select -ter and specify none as termini , it still gives error saying
"There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. " Please help. Error without -ter option: Processing chain 1 'B' (434 atoms, 21 residues) Identified residue DADE1 as a starting terminus. Identified residue DTHY21 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Start terminus DADE-1: NH3+ End terminus DTHY-21: COO- ------------------------------------------------------- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/sucharita/sucharita/softwares/gromacs_all/gromacs-4.6.3/src/kernel/pdb2top.c, line: 1148 Fatal error: atom N not found in buiding block 1DADE while combining tdb and rtp For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors with -ter option selecting none Processing chain 1 'B' (434 atoms, 21 residues) Identified residue DADE1 as a starting terminus. Identified residue DTHY21 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Select start terminus type for DADE-1 0: NH3+ 1: NH2 2: None 2 Start terminus DADE-1: None Select end terminus type for DTHY-21 0: COO- 1: COOH 2: None 2 End terminus DTHY-21: None ------------------------------------------------------- Program pdb2gmx, VERSION 4.6.3 Source code file: /home/sucharita/sucharita/softwares/gromacs_all/gromacs-4.6.3/src/kernel/pdb2top.c, line: 1109 Fatal error: There is a dangling bond at at least one of the terminal ends. Fix your coordinate file, add a new terminal database entry (.tdb), or select the proper existing terminal entry. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Sucharita Dey,PhD, Research Fellow, Cancer Science Institute of Singapore, National University of Singapore. 14, Medical Drive, #12-01, Singapore 117599. Tel: (65) 90355220, email: cs...@nus.edu.sg -- 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.
