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. Author manuscript; available in PMC: 2013 Jul 10.
Published in final edited form as: J Chem Theory Comput. 2012 Jun 15;8(7):2521–2530. doi: 10.1021/ct3003089

Table 1.

Benchmarked protein systems. Listed are associated surface areas, in units Å2, as calculated by NAMD’s and Amber’s implementations of the LCPO54 algorithm.

Name PDB ID # Atoms NAMD SA Amber SA
villin headpiece 1YRI 582 2,706.72 2,706.72
flavodoxin 2W5U 2,412 9,988.72 9,988.72
glycogen phosphorylase 1GPB 13,340 46,106.66 46,106.68
RuBisCO 1IR2 74,926 176,335.86 176,335.90