Re: [AMBER] Give the correct charge to heme using antechamber

From: Elvis Martis <>
Date: Fri, 27 Jan 2017 04:22:38 +0000

Just to add to David's answer.
Manchester database already has two set of HEME parameters, one for all-atom and other for united atoms but I guess they are outdated.
There is an old post regarding this issue,
Moreover, Cheatham et al have published "Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle J Comput Chem. 2012 Jan 15; 33(2): 119-133." which are good enough to be used with amber.
 If inhibitors are to be modeled (as 6th ligand, as is the case with azole type inhibitors), then you must tweak around little (manually possible to add entries to the heme frcmod and prepin files) to yield a combined frcmod and prepin files.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: David Case []
Sent: Thursday, January 26, 2017 10:42 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Give the correct charge to heme using antechamber

On Thu, Jan 26, 2017, Matteo Uggeri wrote:
> my problem is that I can't assign to heme the correct charge using
> antechamber.

I guess I don't understand the question. Antechamber can't handle heme, since it contains an iron atom that is not supported in antechamber.

I'd suggest starting with a heme library that has been used before, e.g.
from the contributed parameters database. If you are unhappy with those charges (which are rather old), you could use MCPB or R.E.D. to generate a new charge distribution.

[Developers: it would be great for someone to collect various heme libraries from the literature, and submit them to the Manchester database (or somewhere else).]


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