Re: [AMBER] MMGBSA error mitigation

From: Debarati DasGupta <>
Date: Sun, 14 Nov 2021 13:13:37 +0000

Dear Prof Case
Your correct!
I Got it to work after stripping all waters and ions, charges do not have to be zero, I was confused as generally before setting the simulations I usually neutralize the complex.
Thank you so much

From: David A Case <>
Sent: Saturday, November 13, 2021 9:52:02 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] MMGBSA error mitigation

On Sat, Nov 13, 2021, Debarati DasGupta wrote:

>One small query regarding creation of prmtop files for MMGBSA type calculations
>Should the dry_complex(non solvated) be neutralized with counterions to
>keep net charge 0 same for receptor prmtop and ligand?

Generally, there should be no mobile ions (cations or anions) and no solvent
molecules in the prmtop files that the MM/pbsa actually uses.

Clearly, the total charge of the (stripped) complex prmtop has to be the
same as the sum of the charges for the receptor and ligand. But none of
these need to be zero. Indeed, they will often not be zero.

I thought this would be the default for ante-mmpbsa, but I've never used
that facility, so others will have to chime in here.


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Received on Sun Nov 14 2021 - 05:30:02 PST
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