From: yandong Huang (ydhuang2727_at_163.com)
Date: Sat Jan 31 2015 - 13:24:55 CST
Hi, NAMD developers,
NAMD uses the Linear Combination of Pairwise Overlaps (LCPO) [1] method to approximate the surface area of molecules.
So far as i know, the parameters of P1-P4 have been re-parametrized by Y. D. Huang et. al. [2] and A. Morreale et. al. [3] in the framework of CHARMM22/CHARMM36 and AMBER force fields respectively.
Besides, Y. D. Huang et. al. further re-parametrized P1-P4 for LCPO/NLR [4] method, in which NLR is a Neighbor List Reduction method to reduce computational cost.
My question is if the parameters P1 to P4 in LCPO that NAMD used are still those from the original paper of LCPO? If yes, could anybody explain why it's feasible? Thanks!
Best,
Yandong Huang,
[1] J. Weiser, P. S. Shenkin, W. C. Still, Approximate Atomic Surfaces from Linear Combinations of Pairwise Overlaps (LCPO), 1999, 20, 217-230
[2] Y. D. Huang, J. W. Shuai, induced dipoles incorporated into all-atom protein simulations with multiple modeling, 2013, 117, 6138-6148
[3] A. Morreale, R. Gil-Redondo, A. R. Ortiz, A new implicit solvent model for protein-ligand docking. Proteins: Structure, Function, and Bioinformatics 2007, 67, 606-616
[4] J. Weiser, A. A. Weiser, P. S. Shenkin, W. C. Still, Neighbor List Reduction: Optimization for Computation of Molecular Van Der Waals and Solvent-Accessible Surface Areas. J. Comput. Chem. 1998, 19, 797-808
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