[gmx-users] pdb2gmx error

Gadzikano Munyuki Gadzikano.Munyuki at uct.ac.za
Wed Mar 19 15:54:41 CET 2008

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
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


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