Re: [AMBER] Perturbing charges

From: Delwakkada Liyanage, Senal Dinuka <>
Date: Fri, 18 Sep 2020 12:57:58 +0000

Thank you very much Dr. Case for reaching out soon. This was a relief to hear. But now I have another doubt.

For the ligand discharging step I have to do TI simulations with start state and ending state. In sander I can group two prmtop for this purpose. If I'm using crgmask to remove charges, shouldn't both of my prmtop be the same?

Senal Dinuka

From: David A Case <>
Sent: Thursday, September 17, 2020 9:12:15 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Perturbing charges

On Thu, Sep 17, 2020, Delwakkada Liyanage, Senal Dinuka wrote:
>I'm trying to derive parameters for a TI state where the ligand is
>supposed to disappear from solvent. I have gone through both the TI
>tutorials A9 and older Amber9 tutorial for toluene disappearance. Given
>that I'm dealing with a fairly large ligand with 90 atoms, I like to
>know if there is any straightforward approach to change charges in xleap
>rather than one by one.

Check out the 'crgmask' paramter (Chap 23), which allows you to easily
set certain charges to zero.

>Also does a amber OFF file holds all the information in a prepi or frcmod file?

An OFF file has the same info as prepi. It does *not* contain force
field paramters that would be in a frcmod file.


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