AMBER Archive (2005)

Subject: Re: AMBER: R.E.D

From: Wai Keat Yam (yamwaikeat_at_yahoo.com)
Date: Sun Mar 06 2005 - 20:31:57 CST

Dear fellows,

Hi. I really appreciate your replies. Thank you very
much.

Wai Keat, Yam (Ms.)
Molecular Simulation & Computation Group (MSC)
Biocrystallography & Structural Bioinformatics
Laboratory
University Science Malaysia,
Minden, 11800 Pulau Pinang,
Malaysia
Tel: 604-6533888 ext. 2437

--- FyD <fyd_at_u-picardie.fr> wrote:

> Dear Wai Keat Yam,
>
> > Hello there. I would like to express my gratitude
> to
> > the development of R.E.D, which has indeed help me
> a
> > lot in calculating charges, to be used in AMBER.
>
> R.E.D. is only the application of the following
> work:
> Cieplak et al. J. Comput. Chem. 1995 16 1357-1377
>
> R.E.D.-II present numerous improvments compared to
> R.E.D.-I (the version you
> have I think) thanks in particular to the AMBER
> mailing discussions. We can send
> you the new version which present a really better
> manual and also new tutorials.
> We worked a lot on the new manual.
>
> > R.E.D works very well with g03, as my input file
> > (minimized structure)was done by g03 and other
> > calculation (MEP) also using g03.
>
> R.E.D. works well with GAMESS-US, g94 (thanks to
> Menno D. & Vlad C.), g98 & g03.
> We will implement the use of GAMESS-UK in R.E.D.-III
> (thanks to the help of
> Thomas P.)
>
> > However,
> > from the output file (mol_o.mol2), I found that 2
> of
> > my H atom (out of 118 atoms) is charging
> negatively
> > (-0.0293, -0.0893). I would like to ask
> > whether this is possible? Could I still use these
> > values in AMBER later??
>
> Yes, here is what we found for the EtOH molecule:
> C5 0.3922
> H6 -0.0545 (methylene group).
>
> > Also, my input file was minimized with B3LYP/6-31G
> > (d,p) and R.E.D used HF/6-31G* to generate MEP
> > calculation. Is this reasonable?
>
> As Piotr answered, only HF/6-31G* is implemented in
> R.E.D.-I since it is the
> theory level which has been used by the Kollman's
> group in the Cornell et al.
> FF development. My understanding is that the
> HF/6-31G* theory level is
> _required_ to compute the MEP (see the manual why).
> However, which theory level
> has to be used for the geom. opt. is less clear for
> me. Personnaly, I use
> B3LYP/6-31G* quite often but _only_ in geom. opt. We
> added information about
> the use of HF/6-31G* in R.E.D. in the R.E.D.-II
> manual.
>
> However, the use of B3LYP instead of HF in geom.
> opt. might have a tricky
> disadvantge: the implementation of the B3LYP method
> in GAMESS & Gausssian is
> different. This means that the RESP (and ESP
> charges) will be different (not
> reproducible) for the same structure/minimum if you
> compare the results
> obtained with 2 QM soft. We ran a lot of tests and
> caraterized which conditions
> give different RESP charges using the 2 QM soft:
> This is summarized in the
> R.E.D. manual version II. Here is what you can find
> in the R.E.D.II manual about
> the use of B3LYP in geom. opt.:
> "Another example is the utilization of the B3LYP
> method in geometry
> optimization. Different mathematical equations for
> this method (based on the
> VWN5 or VWN3 correlation functional) are implemented
> in each program. If this
> method is used to optimize geometries (i. e. the
> R.E.D. code has to be
> modified), it leads to slightly different geometries
> and RESP or ESP charges."
>
> Thank you for this very kind email, regards,
>
> F.-Y. Dupradeau
> DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
> The Scripps Research Institute, La Jolla, CA, USA
> --
> http://www.u-picardie.fr/labo/lbpd/FyD.htm
>
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