[gmx-users] Adding an Oxygen into a Protein Heme Group; advice needed.

Matthew Fisher matthew.fisher at stcatz.ox.ac.uk
Tue Nov 20 02:02:27 CET 2018

Dear all,

I've stumbled across a problem with my input PDB files and I wonder if anyone could advise. For my structure, I need to add a carbonyl oxygen onto the axial position of the HEME group in my protein, which is connected to the protein backbone by a Fe-S bond to a Cysteine protein.

I have Amber Mol2/Frcmod files that I could work with (these do contain the oxygen coordinates), creating the prmtop/inpcrd files in Xleap (which has the added advantage that it will add the missing Oxygen in) and porting via acpype, but I'm concerned I won't be able to maintain the Fe-S bond adequately if I add the Heme in via this methodology (/if it's possible, I'm not sure how you would do it)?

The way I would rather do it, if possible, is add the oxygen into the pdb file and then use pdb2gmx, with the parameters I've already added to the AMBER99SB-ildn force field, to parametise the system, but I was wondering if this would a) yield a good topology and b) how to go about it if possible?

Any advice will be appreciated,


Matthew Fisher

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