Hi Senal,
Amber will assign atoms that match crgmask zero partial charge, its so
simple. So in decharging step you basicly have two copies of same ligand
in your input pdb file and you have to set timask1 to one of them and
timask2 to second one. Then you have to set crgmask to match part of
second ligand (the one that you specified by timask2) that you want to
decharge.
I would recomend you to complete this tutorial
https://ambermd.org/tutorials/advanced/tutorial9/index.html
And be sure you understand timasks scmasks and crgmask.
Juraj
On 28. 10. 20 17:02, Delwakkada Liyanage, Senal Dinuka wrote:
> Dear Amber users,
>
> I have a doubt about using crgmask flag in thermodynamic integration. In a decharging step, if I use crgmask for my ligand, does that mean my ligand charges are already zero?
> Also, if my timask1=':ligand_resname', what should be the timask2?
>
> Thank you
>
> Senal
> _______________________________________________
> 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 Oct 29 2020 - 02:30:03 PDT
