Premium
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
Author(s) -
Kaminski George A.,
Stern Harry A.,
Berne B. J.,
Friesner Richard A.,
Cao Yixiang X.,
Murphy Robert B.,
Zhou Ruhong,
Halgren Thomas A.
Publication year - 2002
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.10125
Subject(s) - ab initio , force field (fiction) , polarizability , quantum , chemistry , molecular dynamics , statistical physics , gas phase , experimental data , computational chemistry , basis (linear algebra) , physics , molecule , quantum mechanics , mathematics , geometry , statistics , organic chemistry
We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic‐size systems. Employing high‐level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas‐phase many‐body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di‐ and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS‐AA force field.1 Finally, we have employed the newly developed first‐generation model in computing gas‐phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed‐charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second‐generation model. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1515–1531, 2002