Dear Sir,
I am trying to learn Thermodynamic Integration calculation using AMBER
software. For that, I am trying to understand the input files for the
transformation of benzene to phenol. I have downloaded the files. But, I
would like to know, in case of initial set-up of the system, *1_leap.sh*
script is using for creating .parm and .rst files for both the ligands and
complex in solution. I mean this step is used for performing MD
simulations to create coordinates for decharging and recharging steps. I
want to know, why vdW + bonded transformation is happening i.e, when AMBER
is recognizing this. It would be really great, if you kindly clarify this.
Thanks and regards
Kankana Bhattacharjee
Ph.D. Scholar
Department of Chemistry
Ashoka University
Sonipat, Haryana
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Received on Tue Apr 30 2024 - 05:00:02 PDT
