Dear James,
> 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?
RED Server Development
http://q4md-forcefieldtools.org/REDServer-Development/ handles all the
elements of the periodic table (but a few ones).
See Tutorial: http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
you will find many examples there; and as usual post queries to the
q4md-fft or Amber mailing list if you encounter problems... We always
try to help.
regards, Francois
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Received on Thu May 08 2014 - 04:30:02 PDT
