Dear sir,
Thank you very much for your kind reply. In practice, we neutralize a system before any MD simulation. But in absolute free energy calculations, I was thinking we should not neutralize the system because we are anyways decharging the system.
Also, if I did a 12-point lambda simulation for decharging, do we check the convergence per lambda trajectory or for the combination of lambda trajectories?
Please let me know your thoughts about these.
Since I'm only decharging a ligand, I'm sampling a lambda point for 10 ns. What would you suggest should I investigate considering the convergence and correctness of the simulation?
Thank you very much for your time.
Senal
________________________________
From: Juraj Dobias <juraj.dobias.uochb.cas.cz>
Sent: Thursday, October 29, 2020 4:04 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Amber TI - crgmask
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://secure-web.cisco.com/18BzDIb__0x_9m-4MOms63gcQmw1O5SbK9D72Slr80DQlw76rLtCfkdU7p_Cv47fRoanpKeCZiU3lRUcWm3SFnQo_we7Ud558hVafjQDSWplpyp-cp4zsvM_0jlIV9sWG9Kb9UU4SRd4pWhv3sYCrRFPlXuMcHQBA_aJPfB7Riv9RN02pD1nTgmxpt7HCknLTPos0qA_Jiry6vaPp5hKOVqTREC6TRpw4rbyeBjYaVqJjDmPk7slhckCA9Bn_IJ7Eqroad-zld_c8MEyE56w39bL33hE4NlWYJ7MKBNTAMhU_M_TjylnLWDDlJDeGFYyV/https%3A%2F%2Fambermd.org%2Ftutorials%2Fadvanced%2Ftutorial9%2Findex.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
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Received on Thu Oct 29 2020 - 08:30:02 PDT
