Dear Arturas,
> I have performed 3 conformation RESP fitting to calculated charges for
> alpha-carboxyl-glutamic acid. I have used as a basis AMBER advance
> tutorial about fluorescein and linker (tutorial A1). What I did I
> capped my residue with ACE and NME groups. Minimized 3 conformations.
> Restrained cap charges as said in the tutorial.
>
> Everything works fine, except CA gets charge 1.2 after RESP fitting.
> Also other atoms in peptidic fragment have larger charges.
It is difficult to answer as you do not provide a lot of information
about the molecular system you are working on. If you get a charge of
1.2 for a CA atom something wrong appends in your strategy, I guess.
There were some intense discussions about this tutorial & I do not
want to reignite any tension. However, you have to be aware that the
fitting step in this tutorial is not correct. This tutorial should
better define the parameters used to help new users to understand the
choices made. This tutorial will be corrected.
> To increase RESP restrain factor ?
You can try, but I do not think so.
> Increase number of points in ESP calculations?
The number of points is already very high in this tutorial, and in
such a case it is not really useful (although you never know as we do
not know very well the type of structures you are working on).
> Or maybe for amino acids (ff99SB) there is another protocol to
> develop charges ?
There is one charge derivation procedure for AMBER force field (that
can be modified when it does not work in some specific cases). My
feeling is that in your case the default charge derivation procedure
for AMBER force field should work. I might be wrong but I think you
made some errors and/or the fitting step of this tutorial generate
artefacts.
> Any suggestion or comments ?
If you want I can run R.E.D. Server for you, apply the AMBER default
charge derivation procedure and see if it works for you. In this case,
just send to my personal email these 3 geometry optimization output
files and I will generate a 4-molecules charge fit using either each
of your conformations taken individually and your three conformations
taken as a single molecule. This will take 10 minutes.
I hope this helps,
regards, Francois
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Received on Fri Jan 30 2009 - 01:33:24 PST
