Hello Prof Roitberg,
I just noticed that and was about to close this thread, thanks for your quick response.
For some reason MolSoft has deprotonated that amide H, I need to maybe check in with them.
Thank you again.
Debarati
________________________________
From: Adrian Roitberg via AMBER <amber.ambermd.org>
Sent: Tuesday, December 31, 2024 10:12 AM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] Antechamber setup for PDS
You are missing an H atom in one of your amide nitrogens, so the system
thinks it should be a radical.
Adrian
On 12/31/24 1:02 PM, Debarati DasGupta via AMBER wrote:
> [External Email]
>
> Hi Amber team,
> Seems like I am making a mistake in my antechamber protocol for this small molecule (PDS). It should not be so complicated. All I have done is docked it and saved the docked pose as a sdf file which I then converted to pdb.
> [cid:4452caa5-3ec9-4c98-b12a-87ddb7d1fbc8]
>
>
> It has 3 basic amines and I would anticipate the net charge is 3 but when I run the antechamber command I get this error:
>
> [cid:1111194d-e767-4766-a294-cfc8db89ec62]
>
>
>
> --------------------------------------------------------
> AMBER SQM VERSION 19
>
> By
> Ross C. Walker, Michael F. Crowley, Scott Brozell,
> Tim Giese, Andreas W. Goetz,
> Tai-Sung Lee and David A. Case
>
> --------------------------------------------------------
>
>
> --------------------------------------------------------------------------------
> QM CALCULATION INFO
> --------------------------------------------------------------------------------
> QMMM: System specified with odd number of electrons ( 237)
> QMMM: but odd spin ( 1). You most likely have the charge of
> QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run calculation.
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Tue Dec 31 2024 - 11:00:02 PST
