[gmx-users] Reg: fatal error pdb2gmx

[Mark Abraham]

On 20/12/2010 4:25 PM, vinothkumar mohanakrishnan wrote:
> Hi all
>
> I want to use pdb2gmx to generate hexane topology and hexane.gro file. 
> i have added the atom name in .atp file and corresponding section in 
> .rtp file. i have given below my .rtp entry

You don't need to add an .rtp entry, it's as much work as writing your 
molecule's .itp file and more fiddly.

>
> [ DRG ]
>  [ atoms ]
> CAA opls_966   0  1
> CAF opls_966   0  1
> CAB opls_967   0  2
> CAC opls_967   0  2
> CAD opls_967   0  2
> CAE opls_967   0  2
>
>  [ bonds ]
> CAA    CAB
> CAB    CAC
> CAC    CAD
> CAD    CAE
> CAE    CAF
>
>  [ angles ]
> CAA    CAB    CAC
> CAB    CAC    CAD
> CAC    CAD    CAE
> CAD    CAE    CAF
>
>  [ dihedrals ]
> CAA    CAB    CAC    CAD
> CAB    CAC    CAD    CAE
> CAC    CAD    CAE    CAF
>
> but i get the error message as given below and it doesn't generate any 
> .top and .gro file . I searched the mailing list and found a similar 
> post but there is no solution 
> (http://oldwww.gromacs.org/pipermail/gmx-users/2009-May/041609.html) 
> previously i used pdb2gmx for other molecules and it worked fine for 
> the oplsaa force field. any help is highly appreciated.
>
> Opening library file ffoplsaa.rtp
> Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
> Opening library file /usr/local/gromacs/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 /usr/local/gromacs/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 vdwradii.dat
> Entries in vdwradii.dat: 28
> Opening library file /usr/local/gromacs/share/gromacs/top/dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file /usr/local/gromacs/share/gromacs/top/electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file /usr/local/gromacs/share/gromacs/top/elements.dat
> Entries in elements.dat: 218
> Reading hexane.pdb...
> Read 6 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 1 residues with 6 atoms
>
>   chain  #res #atoms
>   1 ' '     1      6
>
> All occupancies are one
> Opening library file ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file ffoplsaa.rtp
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: resall.c, line: 279
>
> Fatal error:
> in .rtp file at line:
>
>
> -------------------------------------------------------

Probably you've mangled the file somehow, like editing on a non-unix 
system and not changing the line endings, or transferred zero bytes of 
the file.

PRODRG will be worthless for generating parameters for any force field 
other than that which it targets. See 
http://www.gromacs.org/Documentation/How-tos/Parameterization for 
general advice. I'd suggest throwing away what you've been trying to do, 
and seeking a force field that already has hexane-suitable parameters, 
preferably with someone else having already published using those 
parameters. If your literature search comes up empty, perhaps you should 
choose your force field according to the availability of useful 
parameterization tools (see 
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation), 
rather than inventing some Frankenstein approach that your reviewer is 
likely to just laugh at.

Mark