[gmx-users] OXY not found

Andy Torres torand2000 at gmail.com
Thu Mar 5 19:17:27 CET 2009

Hi, I run pdb2gmx (with all the ff that Gromacs bring by default) on
myoglobin (1A6M.pdb) wich I get from the "protein data bank". and I got the

Fatal error:
Residue 'OXY' not found in residue topology database

I check the ff and I did not found the oxigen molecule.
I saw that somebody allready use this molecule in the mailing list:

On Tue, 18 Jun 2002, Valentin Gogonea

Is there a chance to contact him?
Is this molecule in any other ff?
How can I fix this?
How can I take the OXI and SO4 molecules out of my .pdb file without making
Hopping to be clear.
Thanks in advance

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