[gmx-users] Error by pdb2gmx

[Mark Abraham]

Yanmei Song wrote:
> Dear Justin and Dallas:
> 
> Thank you for your help earlier.
> 
> I made a copy of ffoplsaa.rtp to my working directory and add a new
> residue to it. Then perform the following command:
> 
>  pdb2gmx -f pdms10.pdb -o pdms10.gro -p top.top -i pdms10.itp
> 
> Opening library file /packages/gromacs-3.3.3/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: Encad all-atom force field, using scaled-down vacuum charges
>  8: Encad all-atom force field, using full solvent charges
> 6
> Opening library file ffoplsaa.rtp
> Opening library file /packages/gromacs-3.3.3/share/gromacs/top/aminoacids.dat
> Reading pdms10.pdb...
> Read 45 atoms
> Opening library file /packages/gromacs-3.3.3/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 1 residues with 45 atoms
> 
>   chain  #res #atoms
>   1 'A'     1     45
> 
> All occupancies are one
> Opening library file /packages/gromacs-3.3.3/share/gromacs/top/ffoplsaa.atp
> Atomtype 817
> Reading residue database... (ffoplsaa)
> Opening library file ffoplsaa.rtp
> 
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.3
> Source code file: resall.c, line: 289
> 
> Fatal error:
> in .rtp file at line:
> 
> 

Well that's weird. You should use the "diff" utility on ffoplsaa.rtp 
before and after your modifications and see what that tells you.

If you've edited it on a Windows machine, then you may have line-ending 
issues. If so, use "dos2unix" on the file.

Mark