Re: [AMBER] TI calculation steps

From: Debarati DasGupta <>
Date: Thu, 5 Dec 2019 21:39:29 +0000

So for my individual lambdas for equlibriation and production, I will not be using the “crgmask” flag. But how will the program understand that I am trying to remove all partial charges (de couple the ligand from the environment) from my ligand molecule?

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From: Song, Lin<>
Sent: Thursday, December 5, 2019 4:25 PM
To: AMBER Mailing List<>
Subject: Re: [AMBER] TI calculation steps


If you’re disappearing a molecule in one step, the initial state should be the molecule with full vdW and full charge, the end state should be nothing. So the mask should be : timask1=“molecule”, scmask1=“molecule”, timask2-=“”, scmask2=“”. No crgmask should be used.


> On Dec 5, 2019, at 3:24 PM, Debarati DasGupta <> wrote:
> Hi,
> Page 427 of the Amber18 manual says -----> Alternatively to the two-step process of removing charges from atoms first and then changing the vdW parameters of chargeless atoms in a second TI calculation, sander and pmemd also have a soft core version of the Coulomb equation implemented for single step transformations under periodic boundary conditions. This is automatically applied to all atoms in scmask…”
> If one does single step transformation, will the crgmask flag need to be applied?
> For absolute free energy calculations, disappear molecule….
> My timask2=’’, my scmask2=’’, but I am not sure of the crgmask…
> I have scalpha and a scbeta parameter according to equation 21.7 of the manual, but I am not sure of the usage of crgmask.
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Received on Thu Dec 05 2019 - 14:00:02 PST
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