Thanks you so much. I'll try with this one!
Matteo.
2017-01-27 5:22 GMT+01:00 Elvis Martis <elvis.martis.bcp.edu.in>:
> Hello,
> 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 all-atom and other for united atoms but I guess they are outdated.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, http://archive.ambermd.org/
> 201605/0267.html
> 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
> W www.elvismartis.in
> Skype. adrian_elvis12
>
>
>
>
> -----Original Message-----
> From: David Case [mailto:david.case.rutgers.edu]
> Sent: Thursday, January 26, 2017 10:42 PM
> To: AMBER Mailing List <amber.ambermd.org>
> 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).]
>
> ....dac
>
>
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Received on Wed Feb 01 2017 - 07:00:03 PST
