Dear Rodrigo,
> I was just wondering. What is the difference between using antechamber vs.
> REDDB to generate parameters of a new molecule for MD simulation?
Do you mean Antechamber vs. R.E.D.? (R.E.DD.B. is a database; see
http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D360)
I try to make the answer short because one could write pages & pages
about this topic:
Historically, Amber force fields (FF) are based on the ESP (before
1995) and RESP (after 1995) charge models. The different versions of
the GLYCAM FF also use a RESP charge model.
Antechamber allows charge derivation, FF library building & atom
typing in a simple & fast way: This makes its success. Various charge
derivation approaches (RESP, am1-bcc, Mulliken, Gasteiger, etc... see
the manual) & FF library formats are handled. Charge derivation is
mainly carried out for whole molecules. RESP charge derivation handled
by Antechamber is basic (multiple-orientations, multiple conformations
and molecule molecules as well as molecular fragment cases are not
directly handled).
R.E.D. means "RESP ESP charge Derive" and consequently deals only with
the RESP and ESP charge models because it has been shown these charge
models (& in particular the RESP charge model) have advantages (see
below). R.E.D. handles a single FF library file format (the Tripos
mol2 file format - one is enough) & FF libraries generated by R.E.D.
are FF atom type independent. In short, R.E.D. handles
multiple-orientations, multiple conformations and molecule molecules
in ESP or RESP charge derivation for whole molecules and potentially
for any type of molecular fragments.
See
http://q4md-forcefieldtools.org/RED/History.pdf &
http://www.rsc.org/publishing/journals/CP/article.asp?doi=c0cp00111b
for more information.
More generally, ALL the parameters used by R.E.D. in (the three steps
of) RESP and ESP charge derivation have been rigorously studied making
charge values derived by R.E.D. fully _reproducible_. On the contrary,
I find the approach in Antechamber more than ... blurry (why divcon,
mopac & now sqm for the am1-bcc charge model? why using a
parametrized-based method (am1-bcc) for something that computationally
cost nothing our days? and worst charge equivalencing seems... weired
in some cases, etc...).
Thus, I would like to suggest you to use the R.E.D. Tools. Please,
read the original publications of the Amber force fields and that of
the GLYCAM FF: Kollman et al. 1997, Cheatham et al 1999, Wang et al.
2000, Kirschner et al. 2008 (i.e. ref 41-43 & 47 in PCCP
2010,12,7821). Unfortunately, RESP charge derivation for a set of
molecular fragments remains a complex task (you pay for what you get).
This makes the success of Antechamber (however, one can always find
more simple: the bond increment method in the Accelrys Tools is just
one good example).
These are my personal opinions ;-)
regards, Francois
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Received on Sun Jul 25 2010 - 02:00:03 PDT
