[AMBER] Difference between atomtype s6 and sy?

From: X Sun <egeh00.aol.com>
Date: Mon, 09 Sep 2013 22:16:08 -0600

Dear all,

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"?


Xiaoquan Sun.


X Sun
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Received on Mon Sep 09 2013 - 20:30:03 PDT
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