AMBER Archive (2004)

Subject: RE: AMBER: AMBER charges(Cornell et al JACS, 1995) and R.E.D

From: FyD (fyd_at_u-picardie.fr)
Date: Wed May 12 2004 - 13:01:31 CDT

Dear Mikyung Seo,

> I understood the charges of N, H, C and O are different for terminal and
> central amino acids.
> Look at Cornell et al (JACS, 1995) pg.5190-5191.
> All amino acis in Figure 4 are central(non-terminal) but they don't have
> same
> charges as the ones in blocking groups (ACE, NME) for ARG, PRO, LYS.
> Could you explain why they are different?

It looks like there are three types of CENTRAL amino-acids (AA):
the neutral AA, the acidic AA & the basic AA
I guess, it means different strategies were used for these 3 types of AA: It
makes sense.

See also amberX/examples/resp_charge_fit/peptoid the example described by Piotr
Cieplak: As you can see the restaints are in agreement with the NEUTRAL (&
CENTRAL) AA...

If I well understood, you want to derive RESP charges for neutral ARG. You are
lucky, the way to derive the RESP charges of neutral AA is the way described in
the Cieplak et al. paper ;-) See page 1374-1375, only neutral amino-acids are
reported !

> Could you provide beta version of R.E.D. with new manual for
> multi-conformational RESP fit?

OK tomorrow. No manual is available but I will send you an example with the perl
code...

Regards, Francois

F.-Y. Dupradeau
 --
The Scripps Research Institute, San Diego, CA
Faculte de Pharmacie, UPJV, Amiens, France
 --
http://www.u-picardie.fr/labo/lbpd/fyd.htm
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