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 <br><br>Fatal error:<br>Residue 'OXY' not found in residue topology database<br>
<br>I check the ff and I did not found the oxigen molecule. <br>I saw that somebody allready use this molecule in the mailing list: <br><pre>On Tue, 18 Jun 2002, Valentin Gogonea<br></pre>Is there a chance to contact him? <br>
Is this molecule in any other ff?<br>How can I fix this? <br>How can I take the OXI and SO4 molecules out of my .pdb file without making mistakes?<br>Hopping to be clear.<br>Thanks in advance<br><br>Andy<br>