Hey, > 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... Cheers, Tsjerk > > 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. > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
