I want to do dynamics on a cyclic polypeptide. The peptide contains a residue that is not standard Ornithine. I have added [ORN] to the ffoplsaa.rtp file and the aminoacids.dat file.I have put these in the working directory and also in the library. If I grep these files [ORN] is there but i still get an error message below.Is there some database i am meant to edit.
Opening library file /usr/share/gromacs/top/FF.dat Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges 6 Opening library file ffoplsaa.rtp Opening library file aminoacids.dat Reading FIN.pdb... Read 97 atoms Opening library file /usr/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 14 residues with 97 atoms chain #res #atoms 1 ' ' 14 97 All occupancies are one Opening library file /usr/share/gromacs/top/ffoplsaa.atp Atomtype 817 Reading residue database... (ffoplsaa) Opening library file ffoplsaa.rtp Using default: generating 1,4 H--H interactions Using default: removing impropers on same bond as a proper Residue 51 Sorting it all out... Opening library file /usr/share/gromacs/top/ffoplsaa.hdb Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb Back Off! I just backed up topol.top to ./#topol.top.17# Processing chain 1 (97 atoms, 14 residues) There are 16 donors and 13 acceptors There are 15 hydrogen bonds ------------------------------------------------------- Program pdb2gmx, VERSION 3.3 Source code file: resall.c, line: 438 Fatal error: Residue '0RN' not found in residue topology database ------------------------------------------------------- _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
