[gmx-users] pdb2gmx error

[Justin A. Lemkul]

Quoting Gadzikano Munyuki <Gadzikano.Munyuki at uct.ac.za>:

> 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

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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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