[gmx-users] RE: simulation of a metal binding sites

[Marc Baaden]

Hi,

As mentioned by others, there's really lots of literature out there. I 
thought I mention a recent study we carried out, because it actually 
helped discover some new ion binding sites based on MD. By re-examining 
crystal structures based on these results, we could even find 
experimental evidence for those ions being there. [1]

But actually you didn't tell us which ions you want to simulate? 
Monovalent ions should be sort of ok, although there are differences 
among the forcefields (some original KCl used to crystallize). 
Di-valent ions, in particular Ca2+, are much more tricky. Higher 
charged ones are a nightmare. The higher the charge, the more likely 
you might want things like polarization in your simulation.

There are also some specific forcefields finely parameterized for ions 
based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh
and Piquemal.

Good luck,
  Marc

[1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000

[2] SIBFA (Sum of Interactions Between Fragments Ab initio computed)
http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html


bharat.85.monu at gmail.com said:
>> Thankx for the reply ...
>> Can you refer some papers which can be helpful for me to do MD
>> simulation of proteins with ions ... It will be of great help.. I
>> searched the gromacs user list but couldn't get much material..



-- 
 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