[gmx-users] PDB file problems

Erik Lindahl lindahl at stanford.edu
Mon May 20 19:24:13 CEST 2002

Senthil Kandasamy wrote:

> I have a pdb file generated by CHARMM. The protein has 25 aminoacids 
> and I get the following error when I do pdb2gmx
> ---
> Fatal Error:
> Atom OT1 in residue GLY 25 not found in rtp database while sorting atoms.
> ----
> OT1 is the C-terminal oxygen.
> How do I fix this? 

You can just remove it and only keep the "normal" GLY atoms; grompp will 
generate the terminus automatically for you.



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