[gmx-users] Fatal error: Atom O in residue COC 1 not

[Yunfeng Hu]

I do not know if anything else needs to be done. Here is the error 
message after pdb2gmx -ter or -ighn
...
Looking whether force field file ffG43a1.rtp exists
Opening library file ffG43a1.rtp
Opening library file aminoacids.dat
Reading 1.pdb...
Read 22 atoms
Opening library file /usr/local/gromacs/share/top/xlateat.dat
23 out of 23 lines of xlateat.dat converted succesfully
Analyzing pdb file
There are 1 chains and 0 blocks of water and 1 residues with 22 atoms

   chain  #res #atoms
   1 'X'     1     22

All occupancy fields zero. This is probably not an X-Ray structure
Opening library file /usr/local/gromacs/share/top/ffG43a1.atp
Atomtype 50
Reading residue database... (ffG43a1)
Opening library file ffG43a1.rtp
Residue 97
Sorting it all out...
Opening library file ffG43a1.hdb
Opening library file /usr/local/gromacs/share/top/ffG43a1-n.tdb
Opening library file /usr/local/gromacs/share/top/ffG43a1-c.tdb
Processing chain 1 'X' (22 atoms, 1 residues)
Opening library file /usr/local/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
There are 0 donors and 1 acceptors
There are 0 hydrogen bonds
Fatal error: Atom O in residue COC 1 not found in rtp entry with 22 
atoms
              while sorting atoms