Re: [AMBER] the charge error in amber

From: David A Case via AMBER <>
Date: Thu, 19 Jan 2023 13:13:46 -0500

On Tue, Jan 17, 2023, laura zhang via AMBER wrote:
>I got the following error when running tleap step when setting up a amber
>system including a drug molecule and a protein:

There are at least three separate problems coming up here:

>amber20/bin/teLeap: Warning!
>The unperturbed charge of the unit (-4.998000) is not zero.
>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

You need to look at the leap.log output to see what happened here. It could
be something as simple as having the charge warning come before the ions
were added. If in doubt, use the "summary" action in parmed to see an
overview of what is really in the final prmtop file.

>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.

This was addressed earlier (I think): either use pdb4amber, or manually
change the residue names of residues 74 and 239 to HID.

>FATAL: Atom .R<NILE 2>.A<H 22> does not have a type.
An N-terminal residue should not have an atom named "H". Delete this atom
from the input PDB, and let tleap add back in H1,H2,H3 atoms.

...good luck....dac

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Received on Thu Jan 19 2023 - 10:30:02 PST
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