[gmx-users] Fatal error: Atomtype 'OS' not found!

Yunfeng Hu yunfeng at scripps.edu
Tue Oct 5 19:48:08 CEST 2004

Hi, I used prodrg to obtain a topology file for the ligand and 
generated the complex topology file of a enzyme-ligand complex after 
modifying the enzyme topology file. After adding water box, grompp 
complains about atomtype OS not found which seems strange. I have found 
a similar discussion in the mailing-list before and no final solution 
was offered. Here are the commands I used:

pdb2gmx -merge -f complex.pdb -p complex.top -o complex.gro
editconf -bt cubic -f complex.gro -o complex_h2o.gro -c -d 0.85
genbox -cp complex_h2o.gro -cs spc216.gro -o complex_b4em.gro -p 
grompp -f em.mdp -c complex_b4em.gro -p complex.top -o complex_em.tpr
creating statusfile for 1 node...

checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 279 of the 1225 non-bonded parameter combinations
Cleaning up temporary file grompptjdQeY
Fatal error: Atomtype 'OS' not found!

Thank you for any suggestions.


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