[gmx-users] calcium parameters

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Jul 12 10:20:14 CEST 2011


> What makes you think that the chemical behaviour of divalent Ca ion
> resembles Ca bound to oxygen?

Probably because there's quite a body of literature about
charge-transfer, polarization and partial bond character of calcium
ions with oxygens. But there's not a conclusive answer on how to
approach this in MD simulations. It will certainly not do just copy
something from one force field into another, and it is questionable
whether results from one protein are good enough for another, as it
will depend quite a bit on the local environment. In that sense,
calcium might well be regarded an exotic species. Also beware that you
can't just use Lensink's modified charges, as I'm quite certain he
didn't use CHARMM...



> Check out http://www.gromacs.org/Documentation/How-tos/Parameterization
> Mark
> Of course I will correct charge of Ca+2 and its ligands according to lensink
> thesis for charge transfer effects.
> Thank you very much in advance.
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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