Re: [AMBER] descrepancy in net charge - TI output

From: Delwakkada Liyanage, Senal Dinuka <>
Date: Mon, 30 Aug 2021 14:02:57 +0000

Hello Dr. Case,

Thank you for this clarification. I was confused since I had already charge neutralized the system through tleap prior to these calculations.

I would like one small clarification. According to my system, I have duplicates of the ligand where I specify the charge and vdW removal through "crgmask" and "scmask#". I would like to know when specifying the starting and ending states through "timask#", should I include the DNA residues as well? For example, this is the input for decharging step at "lambda=0.5"

    icfe = 1, clambda = 0.56262, klambda = 1,
    timask1 = ':1-26', timask2 = ':1-25,27',
    ifsc = 0, crgmask = ':27',

residues 26 and 27 are the copies of my ligand.


From: David A Case <>
Sent: Monday, August 30, 2021 7:58 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] descrepancy in net charge - TI output

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.


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