AMBER Archive (2005)

Subject: Re: AMBER: Metals with Amber

From: Marc Baaden (baaden_at_smplinux.de)
Date: Thu Nov 03 2005 - 06:33:34 CST

>>> Bill Ross said:
>> > We are currently interested in doing some MD simulations to study
>> > interactions between the proteins and different metal ions, such as Zn,
>> > Cd or As (identification of possible binding sites?). I would really
>> > appreciate any feedback regarding the current standing of computational
>> > approaches for the modeling of protein interactions with the different
>> > metals ions. Basically, we are wondering how well the current Amber
>> > force field reproduces such interactions?
>>
>> I believe that multivalent ions are considered technically
>> beyond the point charge approximation, not sure whether
>> polarization would solve that. [..]

We investigated some basic behaviour of trivalent cations with Amber [1]
and tested in particular the role of polarization. Inclusion of polarization
certainly improved the results significantly and we got a clearer picture,
but there were still features missing.
As a personal conclusion I'd say that it looked like switching on polarization
as a whole for the complete system might not be sufficient. A fine-tuned
approach (treating different solvation shells differently, including some
specific charge transfer, etc.) could be required.
(But then again looking at trivalent cations is pushing force field limits
 quite a bit)

Marc Baaden

[1] M. Baaden, F. Berny, G. Wipff and C. Madic; "A molecular dynamics and
    quantum mechanics study of M3+ lanthanide cation solvation by acetonitrile:
    the role of cation size, counterions and polarization effects
    investigated.", J. Phys. Chem. A, 104, 2000, 7659-7671. 

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden_at_smplinux.de      -      http://www.baaden.ibpc.fr
 FAX: +33 15841 5026  -  Tel: +33 15841 5176  ou  +33 609 843217

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