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.
....dac
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Received on Wed Jan 12 2022 - 18:00:02 PST
