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 Thu May 08 2014 - 04:30:03 PDT
