[gmx-users] [gmx-user]Error by pdb2gmx

[佘安奇]

Dear Editors:
I used gromacs version 4.0.7. I update ffG45a3.rtp to include my molecule with its rtp in the attached file DRG.txt.And the pdb file of my molecule is mol.txt and also attached. When I used the following command,there is an error! "pdb2gmx_mpi  -ff G45a3 -f  iso-C16.PDB"

Opening library file ffG45a3.rtp
Opening library file /home/gromacs4/share/gromacs/top/aminoacids.dat
Opening library file /home/gromacs4/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 /home/gromacs4/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 /home/gromacs4/share/gromacs/top/vdwradii.dat
Entries in vdwradii.dat: 28
Opening library file /home/gromacs4/share/gromacs/top/dgsolv.dat
Entries in dgsolv.dat: 7
Opening library file /home/gromacs4/share/gromacs/top/electroneg.dat
Entries in electroneg.dat: 71
Opening library file /home/gromacs4/share/gromacs/top/elements.dat
Entries in elements.dat: 218
Reading iso-C16.PDB...
Read 81 atoms
Opening library file /home/gromacs4/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 81 atoms

  chain  #res #atoms
  1 ' '     1     81  

All occupancies are one
Opening library file /home/gromacs4/share/gromacs/top/ffG45a3.atp
Atomtype 1
Reading residue database... (ffG45a3)
Opening library file ffG45a3.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
Residue 96
-------------------------------------------------------
Program pdb2gmx_mpi, VERSION 4.0.7
Source code file: resall.c, line: 344

Fatal error:
in .rtp file in residue DRG at line:

What's up with the resall.c in line 344?
I hope the problem won't bother you too much!
Thank you very much!
 
Angel
 
 


      
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