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marked as the old version so I thought that that method was out of
date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
>
>
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Received on Sun May 11 2014 - 03:30:02 PDT
