AMBER Archive (2009)

Subject: [AMBER] Sulfates parameterization for GAGs in GLYCAM_06

From: Sergey Samsonov (sergeys_at_biotec.tu-dresden.de)
Date: Thu Jun 18 2009 - 08:07:17 CDT

Dear AMBERs,

I'm starting to work with GAGs using GLYCAM_06 force field within
AMBER10 and I have a question related to sulfates parameterization. I
saw answers of Dr. Woods to similar questions in FAQ at GLYCAM page but
they are dated the times of several years ago and maybe now there are
some new solutions coming together with the usage GLYCAM_06 force field.

 From what I've read I found several ways could be used to treat
sulfates parameterization task:

1. to use the parameters from Altona (1994), Ferro (1996) papers for
implementation into force field files.

2. to derive RESP charges for -O-SO3 group using several analogs of
-N-O-S- and -C-O-S- and to average the charges/geometries, to introduce
the parameters from these calculations, and, finally, to proceed tuning
the charge on the atom, next to the parameterized group, leaving the sum
of rest of the charges equal to what it was before the introduction of
the sulfate (f.i. if GlcNAc is used for sulfated 2SGlcNAc, only N charge
of Nac-group is changed, since it is adjacent to the sulfate).

3. to get RESP charges for the whole monosaccharide unit and extract
them for sulfate groups, which, in my opinion, would be not really
proper since charges of other atoms are essentially affected by the
chosen conformation (which is considered in GLYCAM full methodology for
parameterization).

4. to use something already existing if there is something, which I
haven't found yet.

What do you think would be the most appropriate way?

Thank you very much in advance and best regards,

Sergey

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