Re: [AMBER] About the drug charge _antechamber

From: David A Case <>
Date: Wed, 12 Jan 2022 20:51:46 -0500

On Wed, Jan 12, 2022, Arooma Maryam wrote:
>The sum of the charges in the mol2 file is -1, just as you requested
>with the "-nc -1" flag. I'm not sure why you think it "shows 0 charge".
>When I computed the charge for the antechamber output file in PyMOL A, it
>showed me that the overall charge on the compound is zero. In the mol2
>file, O1P and O1A should be -1,-1 respectively and then N2 (drug part)
>making four bonds should be +1. But the antechamber processed file does
>not show any charge.
>Please correct me if I'm wrong.

I don't know what pymol is doing here. Did you feed it a pdb file, or the
mol2 file? In any event, you can add up the charges in the mol2 file for
yourself, and see what total you get...

>I never did the geometry optimization step before, I wonder where I can get
>an idea ABOUT how to turn off geometry optimization.

I agree that it's pretty well hidden: see Section 16.2, item #7.

>Do I have to change command or is it related to loading any module?

Short answer is in my previous email:

>For a di-phosphate system like this one, I'd recommend turning off geometry
>optimization at the bcc step: add -ek "qm_theory='AM1' maxcyc=0" to your
>antechamber run. This will dramatically speed up the sqm calculation, and
>should lead to somewhat better charges.


AMBER mailing list
Received on Wed Jan 12 2022 - 18:00:02 PST
Custom Search