[gmx-users] pdb2gmx error_ resall.c, line: 321

[Mark Abraham]

On 24/01/2011 11:53 PM, udaya kiran wrote:
> Dear GROMACS users,
>
> I have received the following error when trying to convert a pdb file 
> (containing N-methylated L- Leucine residue) to gro format.  I am 
> using ffG53a6 forcefield.
>
>
> Opening library file /usr/local/gromacs/share/gromacs/top/FF.dat
>
> Select the Force Field:
>  0: GROMOS96 43a1 force field
>  1: GROMOS96 43a2 force field (improved alkane dihedrals)
>  2: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
>  3: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
>  4: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
>  5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>  6: [DEPRECATED] Gromacs force field (see manual)
>  7: [DEPRECATED] Gromacs force field with hydrogens for NMR
>  8: Encad all-atom force field, using scaled-down vacuum charges
>  9: Encad all-atom force field, using full solvent charges
> 4
> Opening library file ffG53a6.rtp
> Opening library file aminoacids.dat
> Opening library file 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 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 dgsolv.dat
> Entries in dgsolv.dat: 7
> Opening library file electroneg.dat
> Entries in electroneg.dat: 71
> Opening library file elements.dat
> Entries in elements.dat: 218
> Reading 16L6_6S17_start.pdb...
> WARNING: all CONECT records are ignored
> Read '6S17 ', 39 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 6 residues with 39 atoms
>
>   chain  #res #atoms
>   1 ' '     6     39
>
> All occupancies are one
> Opening library file ffG53a6.atp
> Atomtype 1
> Reading residue database... (ffG53a6)
> Opening library file ffG53a6.rtp
> Using default: not generating all possible dihedrals
> Using default: excluding 3 bonded neighbors
> Using default: generating 1,4 H--H interactions
> Using default: removing impropers on same bond as a proper
>
> *-------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.5
> Source code file: resall.c, line: 321
>
> Fatal error:
> in .rtp file at line:
>
>
> -------------------------------------------------------
> *
>
> Could you please let me know what could be the problem..?

You've broken the format of the .rtp file used in ffG53a6. Use the 
"diff" tool to compare the "before" and "after" versions. Be sure you 
are using unix-style line endings.

Mark
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