AMBER Archive (2008)

Subject: Re: Re: AMBER: AdoMet parameterization with antechamber

From: David A. Case (
Date: Mon Nov 24 2008 - 11:19:54 CST

On Tue, Nov 25, 2008, Jeffrey wrote:
> Thanks so much for your instruction, David.
> When running antechamber with all hydrogens, something strage was observed
> in the output. As in AdoMet, the sulfur atom is a sulfonium resulting in a
> system with 1 net positive charge. But the output message showed that the
> net charge was zero...

> [c0225 sam]$ antechamber -i sam.pdb -fi pdb -o sam.prepin -fo prepi -c bcc -s 2

If you have a net charge, you need to use the "-nc" flag in antechamber.

> Total number of electrons: 210; net charge: 0

However, since you have 210 electrons in a neutral system, you would have 209
electrons with a +1 charge. But antechamber can only handle closed shell
systems with an even number of electrons.

Your SAM structure appears to be missing a proton at the O3' position.


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