AMBER Archive (2008)


From: FyD (
Date: Sat Dec 13 2008 - 01:23:10 CST

Hi Ross,

- If You want a reference for 'standard' charge derivation, you have
it in your own tutorial ;-)
Cieplak, P., Cornell, W.D., Bayly, C., Kollman, P.A., J.Comp.Chem.,
1995, 16(11), 1357-1377 (you even provide the corresponding PDF - even
if you do not have the right to do it). To the best of my knowledge
nobody did better, so far. Charge derivation for standard residues is
well explained is this paper, basis set, constraints etc; although
once again it takes time to get into it as this is a huge/complex &
beautiful work. Well, science is not simple ;-)

- You are the last author of this tutorial; Brent is not. Moreover,
the title of the 1st section of your tutorial is:

"1) Charge Derivation for Non-standard residues"

So please, stop hidding & playing with words, this is clearly written
... "Non-standard residues" not "Dye". This tutorial pretends to deal
with charge derivation for Non-standard residues, or I should go back
to the 1st grade ;-)

- Concerning required tutorials for charge derivation at the AMBER web
site, One might decide to update some web pages allowing the AMBER
community to easily find the tutorials (only
about charge derivation & force field library building) @, and to find R.E.DD.B. which
does not exist! I have no problems to
help/participate/whatever_the_word_is, however, may be using what is
already available might be a good start.

- Between You & me, and about the fitting approach itself in this
tutorial, I do NOT think a student did that by her/himself. Someone
that knows well RESP has done that, I can tell you. Using the option
iqopt=2 + preparing by hand the qout file (which is really awful BTW)
in the 1st stage is very subtil (althought the type of constraint used
is suspicious).

- Finally, yes, writing tutorial takes time, you are right. With Piotr
we have read & re-read our 2 tutorials @ Other people here have also
read them to help. Personnally, I prefer releasing nothing than
something I do not master, & let others more qualified explain what
they know.

regards, Francois

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