Re: [AMBER] Perturbing charges

From: Debarati DasGupta <>
Date: Sun, 20 Sep 2020 20:00:24 +0000

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.

Sent from Mail<> for Windows 10

From: David A Case<>
Sent: 20 September 2020 09:02
To: AMBER Mailing List<>
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.


AMBER mailing list

AMBER mailing list
Received on Sun Sep 20 2020 - 13:30:02 PDT
Custom Search