Quoting Gadzikano Munyuki <[EMAIL PROTECTED]>: > 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 > > ------------------------------------------------------- >
At least the way my font is displayed, it appears you have 0RN (zero-RN), not ORN. Could be wrong, but it might just be a typo in the .pdb file. -Justin > > > > > _______________________________________________ > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
