DOC for GBr6 ****************************************************************************************************** Reference: H. Tjong and H-X Zhou. J. Phys. Chem. B, 111, 3055-3061 (2007). GBr6: A Parameterization-Free, Accurate, Analytical Generalized Born Method Harianto Tjong and Huan-Xiang Zhou Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, Florida 32306 ====================================================================================================== ********* GBr6_v1 ********** GBr6 Analytical GB with r6 analytical integration, salt term is parametrized against linear PB. 1) Input: a qcd file that has the following format: ATOM 117 ARG CZ 9.956 7.027 16.365 0.8368 1.7000 ATOM 117 ARG NH1 9.413 5.821 16.234 -0.8737 1.5500 ATOM 117 ARG HH11 8.416 5.775 16.111 0.4493 1.2000 ATOM 117 ARG HH12 9.984 5.003 16.170 0.4493 1.2000 ATOM 117 ARG NH2 11.282 7.164 16.435 -0.8737 1.5500 ATOM 117 ARG HH21 11.629 8.097 16.610 0.4493 1.2000 ATOM 117 ARG HH22 11.888 6.368 16.415 0.4493 1.2000 ATOM 117 ARG C 6.995 11.119 19.875 0.8557 1.7000 ATOM 117 ARG O 6.102 10.579 20.575 -0.8266 1.5000 ATOM 117 ARG OXT 8.116 11.418 20.280 -0.8266 1.5000 Note that hydrogen atoms must begin with H. A qcd file is chosen as default format because it can be used for UHBD, a Poisson-Boltzmann solver which frequently used in our group. However, it is easy to modify the format in the source (fortran) code into pqr (additional q(=charge) and r(=radius) columns to p(=position) in pdb-like format). 2) The following options (input parameters) must be given in the following order: 2FWH.qcd ! qcd filename 4.0 ! protein dielectric const 78.5 ! water dielectric const 90 ! 1:1 salt concentration in mM 300.0 ! temperature in K 3) Run: ./GBr6_v1.x < inp where the 'inp' file contains the 5-line options stated above. If you need to compile the fortran code with ifort: ifort GBr6_v1.f -o GBr6_v1.x f77 also will work but with slower run time of executable. 4) A sample output: File read : 2FWH.qcd Pdie : 4.000 Sdie : 78.500 Salt(mM) : 90.000 Temperature (K): 300.000 Total atoms : 1830 Net charge : -6.000 Delta Ggbr6 = -532.5074 kcal/mol 5) Note: If you don't have a qcd file, at least you have a pqr file. change_pqr2qcd.x will transform a pqr file to a qcd file. pqr file can be generated by amber from crd/rst file using command: ambpdb -pqr -p topfile < rstfile > ambpdb.out ) Alternatively, use "pdb2pqr" program to generate a pqr from a pdb file (for information go to http://pdb2pqr.sourceforge.net), usage: pdb2pqr --ff amber 2FWH.pdb ambpdb.out Note that radii using pdb2pqr are not Bondi radii. You may change the radii set or may not, but refer to the article (J. Phys. Chem. B 111, 3055) for the accuracy varied by radii used. To transform it into qcd: ./change_pqr2qcd.x mv mol.qcd 2FWH.qcd ****************************************************************************************************** ! This program is free software; you can redistribute it and/or modify ! it under the terms of the GNU General Public License as published by ! the Free Software Foundation; either version 3 of the License, or ! (at your option) any later version. ! ! This program is distributed in the hope that it will be useful, ! but WITHOUT ANY WARRANTY; without even the implied warranty of ! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ! GNU General Public License for more details. ! ! You should have received a copy of the GNU General Public License ! along with this program. If not, see ! . !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! ! If modification was made, PLEASE state it clearly in the source code. ! We are not responsible for third party modifications. ! Thank you. ******************************************************************************************************