We have assigned the spectrum of a small protein that contains a c-type heme (i.e. heme covalently bound to two cysteine thiol groups) using CCPN Analysis. The heme has been included as the HEC moiety (thanks to Wayne Boucher). It was added as the final residue in the molecular system. We have the assignments for the heme resonances and NOEs between the protein and the heme identified within Analysis.
We would now like to calculate the structure using ARIA, via the CCPN Analysis-ARIA interface. By default, the version of ARIA I have installed does not recognise HEC (the heme). I think I need to modify the topology and parameters files that come with ARIA to include HEC. I will also need to create a 'patch' that removes the cysteine Hg and then creates a covalent bond. I probably need to create the psf file manually and then specify this in the xml file that controls ARIA. I have some experience of doing this as I've had to 'trick' ARIA into doing things in the past.
Before I put a lot of effort into doing this, I wonder if there is anyone out there who has used CCPN Analysis/ARIA to calculate a structure with a c-type heme. If there is, would you be willing to share some files with me so that I don't have to reinvent the wheel!
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