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?
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10
From: Song, Lin<mailto:songlin3.chemistry.msu.edu>
Sent: Thursday, December 5, 2019 4:25 PM
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] TI calculation steps
Hi,
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.
Best,
Lin
> On Dec 5, 2019, at 3:24 PM, Debarati DasGupta <debarati_dasgupta.hotmail.com> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!ioFpBMP7lJU!k_0OdEe3Y8KdmJl_ZbSUntjz6tHvovbqhZW_CpoQNS07Dw2rnGnPuqrZOR6f4G_VeSskwBFa$<https://urldefense.com/v3/__http:/lists.ambermd.org/mailman/listinfo/amber__;!ioFpBMP7lJU!k_0OdEe3Y8KdmJl_ZbSUntjz6tHvovbqhZW_CpoQNS07Dw2rnGnPuqrZOR6f4G_VeSskwBFa$>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 05 2019 - 14:00:02 PST
