James,
The general method described in TUTORIAL A1 Old: Building your own Custom
Residues <
http://ambermd.org/tutorials/advanced/tutorial1_orig/index.htm> is
basically the same as described in the newer version Tutorial A1: Setting
up a DNA-Ligand
System<
http://ambermd.org/tutorials/advanced/tutorial1/index.htm>
. 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://ambermd.org/tutorials/advanced/tutorial1_orig/index.htm
> >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://ambermd.org/tutorials/ -- 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
_______________________________________________
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 Sun May 11 2014 - 06:00:04 PDT
