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J Mol Model. 2016 Feb;22(2):47. doi: 10.1007/s00894-016-2909-0. Epub 2016 Jan 27.

COMPASS II: extended coverage for polymer and drug-like molecule databases.

Author information

1
School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China. huaisun@sjtu.edu.cn.
2
School of Chemistry and Chemical Engineering and Key Laboratory of Scientific and Engineering Computing of Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200240, China.
3
Dassault Systèmes BIOVIA, 334 Cambridge Science Park, Cambridge, CB4 0WN, UK.

Abstract

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338-7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.

KEYWORDS:

Force field; Heterocyclic compounds; Polymers; Simulation

PMID:
26815034
DOI:
10.1007/s00894-016-2909-0
[Indexed for MEDLINE]

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