On Mon, Aug 30, 2021, Delwakkada Liyanage, Senal Dinuka wrote:
>
>I have attempted a thermodynamic integration for absolute binding free
>energy estimation. I noticed a difference in the net charge according
>to the ParmEd output and the TI mdout for TI region 1.
?? I don't see any discrepancy.
> Number of triangulated 3-point waters found: 13886
>
> Sum of charges for TI region 1 = 26.00000000
> Assuming uniform neutralizing plasma
>
>
> Sum of charges for TI region 2 = 22.00000000
> Assuming uniform neutralizing plasma
>
>The net charge of :* is 8.0000
ParmEd is reporting the net charge of all residues, ":*". pmemd is reporting
the charges for the TI regions you defined, which are presumably not the
entire system.
....dac
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Received on Mon Aug 30 2021 - 06:00:02 PDT
