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

[udaya kiran]

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..?

yours sincerely,
Uday.
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