Hi James,
To my knowledge no forcefield includes heme parameters. Depending on what you are modelling I would recommend looking into these parameters
http://www.ncbi.nlm.nih.gov/pubmed/21997754 . While they were designed for the various states of CYP450 catalytic cycle they also work on other heme containing proteins. Just make sure you pick the right state that best represents your system.
If you need help using these parameters just let me know and I can provide you with some sample usage and pdb setups.
Best,
Parker
________________________________________
From: James Starlight [jmsstarlight.gmail.com]
Sent: Monday, May 12, 2014 3:05 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Modeling systems with non-standard residues
Brent,
Many thanks for suggestions!
Also I wounder to know if some non-standard residues (for example hem) has
been already included in one of the existing amber's param sets ?
Best,
James
2014-05-11 16:35 GMT+04:00 Brent Krueger <kruegerb.hope.edu>:
> James,
>
> The general method described in TUTORIAL A1 Old: Building your own Custom
> Residues <http://scanmail.trustwave.com/?c=129&d=1_Lw0yBW8gHRztQIw3iUpLSj4t5yH09r2reU9JGblA&u=http%3a%2f%2fambermd%2eorg%2ftutorials%2fadvanced%2ftutorial1%5forig%2findex%2ehtm>
> is
> basically the same as described in the newer version Tutorial A1: Setting
> up a DNA-Ligand
> System<http://scanmail.trustwave.com/?c=129&d=1_Lw0yBW8gHRztQIw3iUpLSj4t5yH09r2ueQ9JaRxg&u=http%3a%2f%2fambermd%2eorg%2ftutorials%2fadvanced%2ftutorial1%2findex%2ehtm>
> . Both tell you how to set up a custom residue, so both should be helpful
> to you in that sense. The newer one has (we feel) a bit more detail about
> how to think about fragments as well as considerations regarding
> appropriate atomic charges; it is a fairly complicated custom residue
> scheme so it should prepare you reasonably well for any of your situations.
>
>
> Cheers,
> Brent
>
>
>
>
>
> On Sun, May 11, 2014 at 6:24 AM, James Starlight <jmsstarlight.gmail.com
> >wrote:
>
> > Thanks for suggestions!
> > I've noticed that TUTORIAL A1 Old: Building your own Custom
> > Residues<http://scanmail.trustwave.com/?c=129&d=1_Lw0yBW8gHRztQIw3iUpLSj4t5yH09r2reU9JGblA&u=http%3a%2f%2fambermd%2eorg%2ftutorials%2fadvanced%2ftutorial1%5forig%2findex%2ehtm
> > >was
> > marked as the old version so I thought that that method was out of
> > date
> > :)
> >
> >
> > James
> >
> >
> > 2014-05-08 15:17 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
> >
> > > On Thu, 2014-05-08 at 10:43 +0400, James Starlight wrote:
> > > > Dear Amber users!
> > > >
> > > > I'm looking for some tutorial where I could find information about
> > > > inclusion of non-standard residues into the system using amber param
> > > sets.
> > > > For instance I need to simulate Rhodopsin which contain co-factor
> > retinal
> > > > covalently attached to the amino acid sequence of the protein.
> Another
> > > > intresting protein for me is GFP with the covalently bonded
> chromophore
> > > > merged both from N and C termi to the rest of the protein. What are
> the
> > > > general workflow of the construction of such systems ? Should I
> > > parametrize
> > > > non standard groups using Amber's CGenFF (or alternatively REDS
> > server)?
> > > > Could some one provide me with the script with the example of
> > integration
> > > > of such non-standard residues?
> > >
> > > Have you looked at the tutorial page? There is a tutorial for almost
> > > everything you say you want to do. http://scanmail.trustwave.com/?c=129&d=1_Lw0yBW8gHRztQIw3iUpLSj4t5yH09r2uOcr5KSxw&u=http%3a%2f%2fambermd%2eorg%2ftutorials%2f --
> you
> > > should familiarize yourself with the material on this page since it can
> > > probably answer many of your questions.
> > >
> > > Also, CGenFF is a CHARMM thing, standing for the Charmm GENeral Force
> > > Field. Amber has the General Amber Force Field (GAFF), and
> > > 'antechamber' is the program responsible for charge derivation and atom
> > > typing.
> > >
> > > R.E.D. is another option for more rigorous RESP-based charge
> derivation.
> > >
> > > HTH,
> > > Jason
> > >
> > > --
> > > Jason M. Swails
> > > BioMaPS,
> > > Rutgers University
> > > Postdoctoral Researcher
> > >
> > >
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> > >
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> >
>
>
>
> --
> _______________________________________________
> Brent P. Krueger.....................phone: 616 395 7629
> Associate Professor................fax: 616 395 7118
> Hope College..........................Schaap Hall 2120
> Department of Chemistry
> Holland, MI 49423
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Received on Mon May 12 2014 - 05:00:02 PDT
