Re: [AMBER] Perturbing charges

From: Delwakkada Liyanage, Senal Dinuka <>
Date: Fri, 18 Sep 2020 21:25:23 +0000

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.
Also, I appreciate it if you could look into my approach so far for this two-state TI integration approach.

I was hoping to create a combined prmtop with the same ligand under two different residue names for the initial state. Then for the decharging step I will use crgmask to zero in one of those residues. V0 will be my original residue and V1 will be my masked residue.

Please correct me in this regard.

Senal Dinuka

From: David A Case <>
Sent: Friday, September 18, 2020 10:02 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Perturbing charges

On Fri, Sep 18, 2020, Delwakkada Liyanage, Senal Dinuka wrote:
>For the ligand discharging step I have to do TI simulations with start
>state and ending state. In sander I can group two prmtop for this
>purpose. If I'm using crgmask to remove charges, shouldn't both of my
>prmtop be the same?

Yes: in this case both prmtop files will be the same.

As an addendum to my earlier email, if you have more complicated changes
to make, use parmed rather than leap. The crgmask parameter in sander
is actually a bit redundant, since you could do the same thing in
parmed, with equal ease.


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Received on Fri Sep 18 2020 - 14:30:02 PDT
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