Re: [AMBER] Non zero ligand warning

From: Kenneth Huang <>
Date: Sun, 31 Jan 2021 13:14:48 -0500


I'd second double checking the output charges to make sure they're zero,
and double checking the input that goes into the RESP part in RED. RED/RESP
is usually good at following the overall charge restraints you give it, but
I think it can hiccup if you miss something in the input.

Otherwise, are you getting the charges on the ligand as a bigger piece, ie
a covalent modification on something like cysteine? In cases like that, I
believe you have to be careful about keeping the charges consistent on the
native 'piece', since RED/RESP will recalculate them to be different than
the native charges.



On Sun, Jan 31, 2021 at 9:25 AM David A Case <> wrote:

> 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 - 10:30:03 PST
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