Re: [AMBER] Defining sulfonyl halide atom type

From: FyD <>
Date: Sat, 03 Mar 2012 19:39:04 +0100

Dear Chris,

If you look in one of the last version of the GLYCAM dat file,
parameters have been introduced for the sulfonamide and sulfate
groups, and the S vdW parameters originally developed for sulfide and
thiol have been extended to sulfate and sulfonamide...

You might decide to adopt a similar approach in your S+ case...
(Although getting new vdW parameters might be more suitable in your

regards, Francois

> I am working with a non-standard residue that has a positively charged
> sulfonyl group:
> O=S+=O (sulfur double bonded to two oxygens and a Carbon)
> I
> C
> I used REDS to derive charge values for the nonstandard residue, but I am
> not sure how to define this sulfur atom type. I have looked through other
> atom types predefined by both Amber and this
> website<>
> and
> cannot seem to find anything to help me define this sulfur by analogy. I
> would like to exhaust this method before trying to define my own atom
> types, so if anyone has any advice on the matter I would be very grateful.
> Thanks,
> Chris Bryant

AMBER mailing list
Received on Sat Mar 03 2012 - 11:00:03 PST
Custom Search