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Coarse-Grained Parameter Files - Printable Version

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Coarse-Grained Parameter Files - jasonlai - 09-27-2012 08:00 AM

From talking with some of you over the summer, I know that you favor the all-atom model with Medusa and no longer support coarse-grained models.

However, in the past, your group has published papers using various types of coarse-graining using DMD. Even though these files are no longer compatible with the latest version of piDMD, I was wondering if I could see those parameter files anyway. It would be really beneficial as a starting point to building my own CG force field so that I don't have to do the parametrization from scratch.


RE: Coarse-Grained Parameter Files - fding - 10-07-2012 12:45 PM

Hi Jason,

The parameters for most of the coarse-grained simulations are recorded in the corresponding papers. I haven't had a time to formalize the parameters for the pDMD package. Based on the tutorial and the parameters in the paper, you can create input files for pDMD simulations.

F. Ding, Dokholyan V.N., Buldyrev V.S., Stanley H.E. and Shakhnovich E.I. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J., 86 (6): December 2002

F. Ding, Borreguero J.M., Buldyrev S.V., Stangley H.E. and Dokholyan N.V., A mechanism for alpha-helix to beta-hairpin transition, Proteins: Structure, Function and Genetics, 53:220-228 (2003)

F. Ding, S. V. Buldyrev, and N. V. Dokholyan, "Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model", Biophys. J., 88: 147-155 (2005).