[gmx-users] Reg: fatal error pdb2gmx

[vinothkumar mohanakrishnan]

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

[ 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:


-------------------------------------------------------

Regards
Vinoth
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101220/4e6482c3/attachment.html>