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Parameterizing the heme in CHARMM-GUI
#38092 10/01/20 06:25 PM
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S
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Hello all,

I've been attempting to build a lipid-bound P450 system with CHARMM-GUI. My lab uses Amber 16 and as such, I've built the system in CHARMM-GUI to use Amber force fields. However, I've been unable to get CHARMM-GUI to recognize the heme in the protein as a heme. On our local machines, we use a .mol2 file that contains the bond information to parameterize the heme, but I've been unable to figure out how to add this file (or any file that contains the heme topology) to CHARMM-GUI. When I simply ignore it and let CHARMM-GUI try to figure out how to parameterize it, CHARMM-GUI always attempts to treat the heme as a ligand and use GAFF (general amber force fields) to parameterize it, which returns an error stating that the residue HEME could not be found or interpreted by GAFF. Any suggestions are welcome!

Thanks!
Sam

Re: Parameterizing the heme in CHARMM-GUI
sratliff118 #38093 10/01/20 06:43 PM
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rmv Online Content
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See the "Reporting CHARMM-GUI problems" post


Rick Venable
computational chemist


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