Force field parameters for METHYL-BACTERIOCHLOROPHYLL-A (bcl) and METHYL BACTERIOPHEOPHYTIN-A (bph) [Ceccarelli et al., J Comp Chem, 2002, pp 2002, 24, pp 129-142]

Published: 8 January 2017| Version 2 | DOI: 10.17632/vwjwp5kxjb.2
Contributors:
Matteo Ceccarelli,
Piero Procacci,
Massimo MARCHI

Description

The file is a gzipped tar archive containing the directory bcl-bph, containing the files: * README: This file. --------------------Force field parameters--------------------------------- * cromo.tpg: the topological definitions of the photosynthetic cofactors "bcl" (methyl-bacteriochlorophyll-a) and "bph" (methyl bacteriopheophytin-a) with atomic types assignment. * cromo.prm: the valence and non bonded parameters of the force field. N.B.: The format and structure of these files is described in the ORAC manual, sec. 10.3, available at the internet address http://www.chim.unifi.it/orac/orac-manual.pdf. The orac code [Procacci, J. Chem. Inf. Model., 2016, 56 (6), pp 1117-1121] can be downloaded from http://www.chim.unifi.it/orac/ under the GPL3 license. ---------------------------------------------------------------------------- --------------------ORAC input files---------------------------------------- * bcl_start.pdb: * bph_start.pdb: The starting PDB structures of bcl and bph (heavy atoms only) with atomic labels that are matched in the topological file cromo.tpg. * bcl.in: * bph.in: The orac input sets for the CG minimization of the structure and harmonic frequencies calculations. ----------------------------------------------------------------------------- -------------------ORAC output files ---------------------------------------- *bcl_min.pdb: *bph_min.pdb: The minimized PDB structures of bcl and bph with hydrogen atoms *bcl.freq: *bph.freq: Harmonic frequencies and corresponding eigenvectors of bcl and bph. N.B: Normal modes can be directly visualized using jmol or xmakemol ------------------------------------------------------------------------------

Files