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Coarse-Grained Parameter Files
09-27-2012, 08:00 AM
Post: #1
Coarse-Grained Parameter Files
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.

Thanks
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10-07-2012, 12:45 PM
Post: #2
RE: Coarse-Grained Parameter Files
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.

2-bead:
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

4-bead:
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)

Pseudo-allatom:
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).
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