Re: [AMBER] Non zero ligand warning

From: David A Case <>
Date: Sun, 31 Jan 2021 09:24:59 -0500

On Sun, Jan 31, 2021, Ayesha Fatima wrote:

>I have a protein-ligand system. For the ligand, i calculated the RESP
>charges using the Pyred server. Then i prepared my files for simulation.
>when I developed the ligand prmtop, amber gave a warning of 0.1239
>unperturbed charge. How do i neutralise this?

First, check the RED/RESP charges for your ligand: do they add up to 0.1239?
Is the ligand supposed to be neutral? If the problem turns out to be the
RESP charges, you will need to make changes at that step.

I can't help with that, but maybe R.E.D. users on the list can chime in, if
they have seen any similar kind of behavior. If the problem is not with the
RESP charges, then we will need to know more details about how you prepared
the ligand prmtop file.

...good luck...dac

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Received on Sun Jan 31 2021 - 06:30:03 PST
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