On Mon, Jul 6, 2015 at 1:33 PM, Arjun Sharma <arjunsharma83.gmail.com>
wrote:
> Dear Amber users,
>
> In AMBER 14 tutorial under Extending CpHMD to additional titratable
> residue section, I see that cpinutil.py file has reference energies
> calculated from different IGB values for cysteine residue. I’m little
> confused as to why do I need to calculate the reference energies with IGB
> values, if I plan to run explicit solvent CpHMD ? Any suggestions are
> appreciated.
>
Because in explicit solvent CpHMD, the titration moves are still done
using GB implicit solvent. I suggest reading the original citation for the
model in detail to make sure you understand it thoroughly. You will need
to if you want to extend it to additional titratable residues.
Good luck,
Jason
http://pubs.acs.org/doi/abs/10.1021/ct401042b <-- citation
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Jul 06 2015 - 11:30:02 PDT
