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

From: Delwakkada Liyanage, Senal Dinuka <sdd313.msstate.edu>
Date: Tue, 31 Aug 2021 22:15:10 +0000

Given what you said, there are very odd values. If residues 1-25 are DNA,
why aren't the net charges negative? Does the ligand have an overall charge
of 4, which might somehow explain the difference between TI region 1 and region 2?

Yes. My ligand has an overall charge of +4. So, the charge difference in TI region 2 is correct. However, it still doesn't explain the positive charge for TI region 1 when DNA is also considered. I analyzed the net charge of DNA through ParmEd and it was given as -23.000. So, with the ligand residue sum of charges for TI region 1 should be -18.00 and TI region 2 should be -22.00. I appreciate your thoughts regarding this.

Senal
________________________________
From: David A Case <dacase1.gmail.com>
Sent: Monday, August 30, 2021 3:07 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] descrepancy in net charge - TI output

On Mon, Aug 30, 2021, Delwakkada Liyanage, Senal Dinuka wrote:
>
>Thank you for this clarification. I was confused since I had already charge
>neutralized the system through tleap prior to these calculations.

Since parmed is reporting a non-neutral system, you might want to
investigate what happened at the tleap stage.

>
>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,
> ifsc = 0, crgmask = ':27',
>
>residues 26 and 27 are the copies of my ligand.

Generally, you want the TI regions to be small, and not include atoms that
are not changing between the end states. IF the DNA residues are unchanged
between the two end states, you (generally) don't want them to be in the TI
regions. Others may have other things to advise here, since I don't do very
many TI calculations any more.

>> Sum of charges for TI region 1 = 26.00000000
>> Sum of charges for TI region 2 = 22.00000000

Given what you said, there are very odd values. If residues 1-25 are DNA,
why aren't the net charges negative? Does the ligand have an overall charge
of 4, which might somehow explain the difference between TI region 1 and
region 2?

....dac

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