AMBER Archive (2007)

Subject: Re: AMBER: AMBER parametrization (??) for OAA and Mg++

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• In reply to: Eduardo Mendez: "AMBER: AMBER parametrization (??) for OAA and Mg++"
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Quoting Eduardo Mendez <pckboy_at_gmail.com>:

> I was wondering if someone can share parameters for the Mg2+ ion, and
> for Oxalate anion (OAA) ?
> I looked at http://pharmacy.man.ac.uk/amber/ and could not find those
> in there :(

You could _very_ easily derive your own parameter using R.E.D.
http://q4md-forcefieldtools.org/RED/.
You have similar models in R.E.DD.B. http://q4md-forcefieldtools.org/REDDB/
See the Ethanoic acid project for instance, W-34
See also the project W-46 for a more complex example.

I just ran R.E.D. on oxalate. On my laptop, it tooks 4 min 20 to get
optimized, 1 min 35 to get the frequencies. Then, R.E.D. took 1 min 35
to get the RESP charges + topology... This is a 10 min work maximum
with R.E.D. counting the structure building with XLEaP...

> Also I noticed the parameter files in that website are set according to
> the amber94 force field, does anyone know where I
> can find parametrization files in agreement with the ff03 forcefield?
> I am specifically looking for ATP, GTP, ADP and GDP

We are about to release in R.E.DD.B. several complex force field
topology databases (FFTPDB),
among them a general force field for "XYP"
              X = A, T, C, G and U
              Y = M, D, T, Q etc...
for the Cornell et al. force field & its different adaptations...

Generating the same FFTPDB, for the Duan et al. FF is straightforward.
That being said, if you look at the Duan et al FF, I think the
terminal aminoacid fragments (AA) come from the Cornell et al. FF
because terminal AA are supposed to be exposed to the solvent. So you
might check which FF model is the best for ATP, GTP, ADP and GDP in
your case.

regards, Francois

PS
I just sent the oxalate data to your own email...

We are working on setting a web server which would run R.E.D....

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• In reply to: Eduardo Mendez: "AMBER: AMBER parametrization (??) for OAA and Mg++"
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