Re: [AMBER] Perturbing charges

From: David A Case <>
Date: Sun, 20 Sep 2020 09:01:40 -0400

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.


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Received on Sun Sep 20 2020 - 06:30:03 PDT
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