Well.
I am not sure but I think you can do both the steps as 1 step protocol in pmemd.cuda, there is no need to do them separately... I have a prmtop file with the ligand in the protein and that’s all, I do not have another copy of the ligand under a different name, maybe I am wrong. Hopefully the xperts will have some hints. I have set timask1=’EOH’ timask2=’’ scmask1=’EOH’ scmask2=’’ respectively in my runs...
Also I have not used crgmask as I am doing both steps as one.
From: Delwakkada Liyanage, Senal Dinuka<mailto:sdd313.msstate.edu>
Sent: 21 September 2020 14:35
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Perturbing charges
Thank you Dr. DasGupta for reaching out. I went through your suggestion and as for the clarification purpose please let me know if I'm correct.
For the removal of electrostatic step, I will be needing a prmtop which includes my ligand and its copy (under 2 residues names). Then I can use 'crgmask' and set charges to 0 in one of them. For this set of calculation with sufficient lambda windows 'scmask' will be set to blank (softcore potential is not used).
For the removal of vdW step, the same prmtop will be used while turning on 'scmask1' and 'scmask2' for the two residues respectively.
Looking forward to hearing from you soon.
Senal Dinuka
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Sunday, September 20, 2020 3:00 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Perturbing charges
Hello Senal Dinuka
For absolute free energy calculations I do not think you need to use the tiMerge option. The timasks are important and the scmasks.
I have not used tiMerge in disappearing a molecule type TI runs. I may be wrong and hopefully experts on the forum can correct me on this.
Debarati
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From: David A Case<mailto:david.case.rutgers.edu>
Sent: 20 September 2020 09:02
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] Perturbing charges
On Fri, Sep 18, 2020, Delwakkada Liyanage, Senal Dinuka wrote:
>Thank you very much for your suggestion, Dr. Case. I'm struggling with
>how to implement this approach with pmemd. I followed the tutorial
>and they have considered two different molecules combine in a single
>prmtop. But in my case since I'm trying to disappear the ligand and I'm
>lost as to how to form a combined prmtop with the part which have vdW
>while the other doesn't.
It's unclear what tutorial you are following here. The pmemd approach
is described in Section 23.1.8 of the manual, and uses the tiMerge
facility in parmed.
I'm not sure if/how crgmask works in pmemd. Others can chime in here.
As I noted before, the "change" action in parmed, which I think would be
used after tiMege, might help. But there are plenty of people on the
list who have done this more than I have, so I hope they will contribute
to the discussion.
....dac
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Received on Mon Sep 21 2020 - 13:00:02 PDT
