[gmx-users] PDB file problems

[Erik Lindahl]

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.

Cheers,

Erik