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 following
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 mistakes? Hopping to be clear. Thanks in advance Andy
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