Re: [AMBER] Perturbing charges

From: David A Case <>
Date: Fri, 18 Sep 2020 11:02:40 -0400

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 - 08:30:02 PDT
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