[gmx-users] Error by pdb2gmx

[Mark Abraham]

Justin A. Lemkul wrote:
> 
> Then it seems clear to me that your installation of Gromacs is faulty.  
> Have you tried running the test set (available on the wiki site)?  If 
> you can describe your computer system (OS, version, compilers used, 
> configuration options, etc.) then perhaps someone on the list can spot a 
> potential pitfall.
> 
> -Justin
> 
> Yanmei Song wrote:
>> Dear Justin:
>>
>> Thank you so much for your help earlier. I updated my GROMACS to
>> 4.0.4. When I run pdb2gmx using the following two files. I still got
>> the similar error message:
>>
>> Opening library file ffoplsaa.rtp
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/aminoacids.dat
>> WARNING: masses will be determined based on residue and atom names,
>>          this can deviate from the real mass of the atom type
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/atommass.dat
>> Entries in atommass.dat: 178
>> WARNING: vdwradii will be determined based on residue and atom names,
>>          this can deviate from the real mass of the atom type
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/vdwradii.dat
>> Entries in vdwradii.dat: 28
>> Opening library file /packages/gromacs-4.0.4/share/gromacs/top/dgsolv.dat
>> Entries in dgsolv.dat: 7
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/electroneg.dat
>> Entries in electroneg.dat: 71
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/elements.dat
>> Entries in elements.dat: 218
>> Reading pdms2.pdb...
>> Read 13 atoms
>> Opening library file 
>> /packages/gromacs-4.0.4/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 3 residues with 13 atoms
>>
>>   chain  #res #atoms
>>   1 ' '     3     13
>>
>> All occupancies are one
>> Opening library file 
>> /packages/gromacs-4.0.4/share/gromacs/top/ffoplsaa.atp
>> Atomtype 1
>> Reading residue database... (ffoplsaa)
>> Opening library file ffoplsaa.rtp
>>
>> -------------------------------------------------------
>> Program pdb2gmx_d, VERSION 4.0.4
>> Source code file: resall.c, line: 279
>>
>> Fatal error:
>> in .rtp file at line:
>>
>>
>> -------------------------------------------------------

This error is being provoked at the top of the .rtp file when a line 
with something like "[header]" is not parsing suitably. A while ago I 
suggested using diff on the .rtp file. Do that.

Mark