Hi,
I would recommend you look at this tutorial:
https://ambermd.org/tutorials/advanced/tutorial39/index.php
It’s listed as Advanced but it’s probably the most up-to-date TI tutorial we have.
Maria
> On Apr 30, 2024, at 7:38 AM, Kankana Bhattacharjee via AMBER <amber.ambermd.org> wrote:
>
> 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 - 08:00:02 PDT
