Re: [AMBER] the charge error in amber

From: Carlos Simmerling via AMBER <>
Date: Tue, 17 Jan 2023 16:06:25 -0500

here the charge is not the fatal error, it is the naming of atoms. HIE has
hydrogen at the epsilon nitrogen, so it should not have atom HD1. You
should check to see how you built the pdb file that you used as input. Did
it already contain hydrogen atoms? If so, and the residue was named HIS, it
may have automatically been converted to HIE. If you know that it should be
HID, you can rename it to HID before loading into leap. the cpptraj
"prepareforleap" command can be helpful for this in the general case (see, but for this one error you
can fix it manually with the renaming. Once again though, it depends on the
source of the pdb file and if you are confident that it is indeed HID not

On Tue, Jan 17, 2023 at 1:16 PM laura zhang via AMBER <>

> Dear Amber users,
> I got the following error when running tleap step when setting up a amber
> system including a drug molecule and a protein:
> amber20/bin/teLeap: Warning!
> The unperturbed charge of the unit (-4.998000) is not zero.
> FATAL: Atom .R<HIE 239>.A<HD1 18> does not have a type.
> FATAL: Atom .R<HIE 74>.A<HD1 18> does not have a type.
> FATAL: Atom .R<NILE 2>.A<H 22> does not have a type.
> But I used the following in the tleap script to neutralize the charge of
> the solvated system:
> addions solvcomplex Cl- 0
> addions solvcomplex Na+ 0
> I am wondering where was wrong and why the net charge of the system was
> not zero. Thank you very much.
> Laura
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Received on Tue Jan 17 2023 - 13:30:02 PST
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