On Tue, Apr 30, 2024, Kankana Bhattacharjee via AMBER wrote:
>
>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.
Are you following the sander or the pmemd path here? The answer also
depends on whether you are doing a "one-step" or "three-step" approach, as
described here:
https://ambermd.org/tutorials/advanced/tutorial9/index.html#overview
Most people (?!) choose the one-step approach, that simultaneously changes
charges and vdW parameters. Try that first, as it avoids complications
(even if fairly minor ones) in the three-step approach.
...good luck...dac
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Received on Fri May 03 2024 - 09:30:03 PDT
