TY - JOUR

T1 - Algorithms for calculating excluded volume and its derivatives as a function of molecular conformation and their use in energy minimization

AU - Kundrot, Craig E.

AU - Ponder, Jay W.

AU - Richards, Frederic M.

PY - 1991/4

Y1 - 1991/4

N2 - A numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln(N) seconds of CPU time on a VAX‐8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure‐volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 105 Pa). R.m.s. gradients of 10−4 kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure‐induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X‐ray crystallography.

AB - A numerical method for calculating the volume of a macromolecule and its first and second derivatives as a function of atomic coordinates is presented. For N atoms, the method requires about 0.3 N ln(N) seconds of CPU time on a VAX‐8800 to evaluate the volume and derivatives. As a test case, the method was used to evaluate a pressure‐volume energy term in energy minimizations of the protein lysozyme at 1000 atm (1 atm = 1.013 × 105 Pa). R.m.s. gradients of 10−4 kcal/mol/Å were obtained at convergence. The calculated structures exhibited pressure‐induced changes which were qualitatively similar to the changes observed in the 1000 atm structure determined by X‐ray crystallography.

UR - http://www.scopus.com/inward/record.url?scp=84986533794&partnerID=8YFLogxK

U2 - 10.1002/jcc.540120314

DO - 10.1002/jcc.540120314

M3 - Article

AN - SCOPUS:84986533794

SN - 0192-8651

VL - 12

SP - 402

EP - 409

JO - Journal of Computational Chemistry

JF - Journal of Computational Chemistry

IS - 3

ER -