Re: [AMBER] Difference between atomtype s6 and sy?

From: David A Case <>
Date: Fri, 13 Sep 2013 09:06:05 -0400

On Mon, Sep 09, 2013, X Sun wrote:
> I am doing simulations about ionized sulphonic acid and netural
> sulphonic acid in TIP3P waterbox with GAFF. I found the atomtype for
> sulfur was different. In the ionized sulphonic acid system, it's
> "s6". But in the netural system, it's "sy". I checked the leaprc.gaff
> file and found the two atomtypes were both "sp3". And in gaff.dat file,
> the nonbond information were the same. Why did Amber make two different
> atom types of sulfur with the same parameters? Was it right to determine
> the sulfur in sulphonic acid as "s6" or "sy"?

As always, you should treat the atom assignments from antechamber as
suggestions. Try both atom types assignments, and see which better fits
data that you have (e.g. from experiment, or quantum calculations.

Note that sy and s6 do *not* have the "same parameters". The nonbonded terms
are the same (as you note) but not the bonded terms.


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Received on Fri Sep 13 2013 - 06:30:04 PDT
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