[gmx-users] adding atom in .atp file

Magnus Andersson magnus.andersson at chembio.chalmers.se
Sun Dec 11 16:07:34 CET 2005

Hi all,

After adding iodine to the ffG43a1.atp file I get the following 'error
message' when running pdb2gmx:

Looking whether force field file ffG43a1.rtp exists
Opening library file ffG43a1.rtp
Opening library file /usr/share/gromacs-3.2.1/top/aminoacids.dat
Reading transiodoretinal.pdb...
Read 4753 atoms
Opening library file /usr/share/gromacs-3.2.1/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 1 blocks of water and 3116 residues with 4753 atoms

  chain  #res #atoms
  1 ' '  3090   4675
  2 '-'    26     78  (only water)

All occupancies are one
Opening library file /usr/share/gromacs-3.2.1/top/ffG43a1.atp
Atomtype 50  (which is my newly added iodine...)

And it just stops... so I guess it's not really an error message. What can
be wrong here?

Cheers / Magnus

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