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?
TFH,
James
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Received on Thu May 08 2014 - 00:00:05 PDT
