[gmx-users] error in pdb2gmx

[Mark Abraham]

Dmitriy Golubobsky wrote:
> Please, give an adive.
> 
> I've add new residues to ffoplsaa.rtp
> build pdb file.
> and try to convert it to gromacs format.
> under WindowsXP, using GROMACS 3.2.1 everyting is OK.
> but, when i did the same comman under GROMACS 3.3.1 (SuSE),
> i've got an error:
> 
> Read 4904 atoms
> Opening library file /usr/local/gromacs/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 258 residues with 4904 atoms
> 
>   chain  #res #atoms
>   1 ' '   258   4904
> 
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.atp
> Atomtype 817
> Reading residue database... (ffoplsaa)
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.rtp
> -------------------------------------------------------
> Program pdb2gmx, VERSION 3.3.1
> Source code file: resall.c, line: 289
> 
> Fatal error:
> in .rtp file at line:
> 
> 
> -------------------------------------------------------
> 
> "These Gromacs Guys Really Rock" (P.J. Meulenhoff)
> 
> 
> What I'm doing wrong?

This is only a guess, but if your .rtp file uses Windows line-endings 
and pdb2gmx is sensitive to that, you might see such a problem. Use 
dos2unix on all your ex-Windows files and see how you go.

Mark