Hi Morteza,
I’ve been doing some simulations on CYPs and using HEME parameters from Shahrokh et al 2012 (
http://www.ncbi.nlm.nih.gov/pubmed/21997754); The supplementary section has the penta-cordinate high spin as well as the dioxygen bound states for HEM, as well as the corresponding cys residues for the S-Fe bond.
You can email me if you need more info about setting up the molecule in tleap, etc - I’ve messed up enough times along the way to be able to diagnose any problems you will likely come across.
Regards,
Kavin
-----------------------------
Kavin Abelak
PhD Student
Comparative Biomedical Sciences
Royal Veterinary College
4 Royal College St
London NW1 0TU
On 14 May 2016, at 14:16, David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>> wrote:
On Fri, May 13, 2016, Morteza Chehel Amirani wrote:
Just wondering where the old HEM parametrization files are located? It
seems they are removed from the current version i.e., 16.
They are at the contributed parameters database:
http://sites.pharmacy.manchester.ac.uk/bryce/amber
Unfortunately, frcmod.hemall file is missing two lines at the end, and I
haven't got the update posted yet. The frcmod.hemall file should end like
this:
NONBON
FE 1.20000 0.05000 0.00000
LO 1.60000 0.20000 0.00000
LC 1.85 0.12 0.0
NP 1.8240 0.1700 OPLS
NO 1.8240 0.1700 OPLS
...good luck....dac
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Received on Wed May 18 2016 - 05:30:08 PDT
