AMBER Archive (2007)

Subject: Re: AMBER: Gaff Charge

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 17 2007 - 00:18:17 CDT

On Mon, Jul 16, 2007, Colby C wrote:

> I have been having trouble running energy minimization with a protein
> inhibitor. There are always super small EEL (large negative) values
> after about 1000 steps which causes SANDER to stop.

This usually means that two atoms are on top of each other...take a look
at the final structure. Do you have hydrogens in your structure with
no vdW (Lennard-Jones) terms?

>
> However I fixed this problem by correcting the charges in the MO2 file
> produced by antechamber. I took charges from the CVF force field from
> insightII. It took a while but SANDER seems to like these charges.
>
> Why doesn't antechamber give me the right charges for my inhibitor?
> (I tried all the antechamber charge options)

Without more information, we can't tell whether the antchamber charges are
"right" or not. Since your note doesn't say what is different between the CVF
charges and the antechamber charges, I'm sure that you can appreciate that
nobody will be able to really provide much help here.

...dac

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