Dear Amber users,
I would like to run MD simulation for cytochrome complex but I am facing a problem with the HEM force field.
As you know, Antechamber, can't be used for that because of the Fe atom.
I found some articles about that such as,
J. Phys. Chem. B 2008, 112, 8165–8173
Chem. Rev. 2004, 104, 3947-3980
J. Am. Chem. SOC1.9 93,115, 9620-9631
Also, I tried to use the force field found by Bryce Group, (heme-all-atom)
http://www.pharmacy.manchester.ac.uk/bryce/amber
So every time, xleap of amber8 gives a long list of missing parameters, something like:
FATAL: Atom .R<HEM 493>.A<CHA 1> does not have a type.
FATAL: Atom .R<HEM 493>.A<CHB 2> does not have a type.
FATAL: Atom .R<HEM 493>.A<CHC 3> does not have a type.
FATAL: Atom .R<HEM 493>.A<CHD 4> does not have a type.......
......
FATAL: Atom .R<HEM 493>.A<NA 39> does not have a type.
FATAL: Atom .R<HEM 493>.A<NB 40> does not have a type.
FATAL: Atom .R<HEM 493>.A<NC 41> does not have a type.
FATAL: Atom .R<HEM 493>.A<ND 42> does not have a type.
FATAL: Atom .R<HEM 493>.A<FE 43> does not have a type.
I would be very grateful for any help or advice.
Thank you very much in advance.
Regards
Hassan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 30 2012 - 18:00:02 PDT
