1 2 3---------------------------------------------------------------------- 4 APBS -- Adaptive Poisson-Boltzmann Solver 5 Version 0.5.1 6 7 Nathan A. Baker (baker@biochem.wustl.edu) 8 Dept. Biochemistry and Molecular Biophysics 9 Center for Computational Biology 10 Washington University in St. Louis 11 12 Additional contributing authors listed in the code documentation. 13 14 Copyright (c) 2002-2007. Washington University in St. Louis. 15 All Rights Reserved. 16 Portions Copyright (c) 1999-2002. The Regents of the University of 17 California. 18 Portions Copyright (c) 1995. Michael Holst. 19 20 This program is free software; you can redistribute it and/or modify 21 it under the terms of the GNU General Public License as published by 22 the Free Software Foundation; either version 2 of the License, or 23 (at your option) any later version. 24 25 This program is distributed in the hope that it will be useful, 26 but WITHOUT ANY WARRANTY; without even the implied warranty of 27 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 28 GNU General Public License for more details. 29 30 You should have received a copy of the GNU General Public License 31 along with this program; if not, write to the Free Software 32 Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 33 34 Linking APBS statically or dynamically with other modules is making a 35 combined work based on APBS. Thus, the terms and conditions of the GNU 36 General Public License cover the whole combination. 37 38 SPECIAL GPL EXCEPTION 39 In addition, as a special exception, the copyright holders of APBS 40 give you permission to combine the APBS program with free software 41 programs and libraries that are released under the GNU LGPL or with 42 code included in releases of ISIM, Ion Simulator Interface, PMV, 43 SMOL, VMD, and Vision. Such combined software may be linked with APBS and 44 redistributed together in original or modified form as mere aggregation 45 without requirement that the entire work be under the scope of the GNU 46 General Public License. This special exception permission is also extended 47 to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG, 48 FEtk, MC, or MALOC libraries. 49 50 Note that people who make modified versions of APBS are not obligated 51 to grant this special exception for their modified versions; it is 52 their choice whether to do so. The GNU General Public License gives 53 permission to release a modified version without this exception; this 54 exception also makes it possible to release a modified version which 55 carries forward this exception. 56---------------------------------------------------------------------- 57 APBS uses FETK (the Finite Element ToolKit) to solve the 58 Poisson-Boltzmann equation numerically. FETK is a portable collection 59 of finite element modeling class libraries written in an object-oriented 60 version of C. It is designed to solve general coupled systems of nonlinear 61 partial differential equations using adaptive finite element methods, 62 inexact Newton methods, and algebraic multilevel methods. More information 63 about FEtk may be found at <http://www.FEtk.ORG>. 64---------------------------------------------------------------------- 65Please cite your use of APBS as: 66 67 Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of 68 nanosystems: application to microtubules and the ribosome. Proc. 69 Natl. Acad. Sci. USA 98, 10037-10041 2001. 70 71 72This executable compiled on Sep 12 2007 at 10:43:13 73 74Parsing input file solvation-apbs-vac-debug.in... 75Parsed input file. 76Got paths for 1 molecules 77Reading PQR-format atom data from 2ala.pqr. 78 22 atoms 79 Centered at (4.112e+00, 4.824e+00, -6.205e-01) 80 Net charge -2.78e-17 e 81Preparing to run 2 PBE calculations. 82---------------------------------------- 83CALCULATION #1 (elec): MULTIGRID 84 Setting up problem... 85 Using cubic spline charge discretization. 86 Grid dimensions: 33 x 33 x 33 87 Grid spacings: 0.500 x 0.500 x 0.500 88 Grid lengths: 16.000 x 16.000 x 16.000 89 Grid center: (4.112, 4.824, -0.620) 90 Multigrid levels: 4 91 Molecule ID: 1 92 Linearized traditional PBE 93 Single Debye-Huckel sphere boundary conditions 94 0 ion species (0.000 M ionic strength): 95 Solute dielectric: 2.000 96 Solvent dielectric: 1.000 97 Using spline-based surface definition;window = 0.300 98 Temperature: 298.150 K 99 Electrostatic energies will be calculated 100 All-atom solvent forces will be calculated 101---------------------------------------- 102CALCULATION #2 (npolar): APOLAR 103---------------------------------------- 104PRINT STATEMENTS 105print force 1 (elec) end 106 Printing per-atom forces (kJ/mol/A). 107 Legend: 108 tot n -- Total force for atom n 109 qf n -- Fixed charge force for atom n 110 db n -- Dielectric boundary force for atom n 111 ib n -- Ionic boundary force for atom n 112 tot all -- Total force for system 113 qf 0 6.281531888568E-01 1.854065155912E+01 2.601074818912E+00 114 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 115 db 0 3.978670072302E-01 -2.955501678650E-01 8.437566864254E-03 116 tot 0 1.026020196087E+00 1.824510139126E+01 2.609512385776E+00 117 qf 1 -3.207752850281E+01 1.290548520883E+01 3.474050266118E+01 118 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 119 db 1 8.279312685094E-02 -6.130512335850E-02 1.776396612354E-02 120 tot 1 -3.199473537596E+01 1.284418008547E+01 3.475826662730E+01 121 qf 2 3.640819124527E+00 -4.227619662527E+00 -1.249140754411E+01 122 ib 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 123 db 2 -3.803208461395E-02 5.128921540299E-02 1.248824363217E-01 124 tot 2 3.602787039913E+00 -4.176330447124E+00 -1.236652510779E+01 125 qf 3 3.824667021045E+00 -4.415893300564E+00 1.321390767889E+01 126 ib 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 127 db 3 -3.745462415223E-02 4.914202559273E-02 -1.326407042979E-01 128 tot 3 3.787212396892E+00 -4.366751274971E+00 1.308126697459E+01 129 qf 4 1.522075369197E+01 -1.440108764898E+02 8.632147965005E+01 130 ib 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 131 db 4 2.030767269246E-01 -3.584099546484E-01 1.232547759522E-01 132 tot 4 1.542383041889E+01 -1.443692864444E+02 8.644473442600E+01 133 qf 5 -1.537063794172E+02 1.370291645540E+02 8.684144824573E+01 134 ib 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 135 db 5 2.123927217121E+00 -2.439202362842E+00 6.170719625099E-01 136 tot 5 -1.515824522001E+02 1.345899621912E+02 8.745852020824E+01 137 qf 6 -9.356291508109E+01 4.346618757585E+01 4.915716177506E+01 138 ib 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 139 db 6 -2.503855324163E+00 1.753622795155E+00 -1.898465801595E-02 140 tot 6 -9.606677040525E+01 4.521981037101E+01 4.913817711705E+01 141 qf 7 7.726933036804E+01 -1.877624592318E+01 1.606406530828E+01 142 ib 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 143 db 7 -1.169197849371E-01 8.923760189439E-02 -3.018267164292E-02 144 tot 7 7.715241058311E+01 -1.868700832129E+01 1.603388263663E+01 145 qf 8 -2.443495416567E+00 -5.737917678027E+00 -1.814748525434E+00 146 ib 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 147 db 8 1.028296687587E-01 -1.062752474568E-01 1.689674823910E-01 148 tot 8 -2.340665747808E+00 -5.844192925484E+00 -1.645781043043E+00 149 qf 9 -2.776309828221E+00 -6.049952556061E+00 2.785679768683E-01 150 ib 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 151 db 9 2.613971809668E-01 -4.503768624191E-01 3.431175126559E-01 152 tot 9 -2.514912647255E+00 -6.500329418480E+00 6.216854895242E-01 153 qf 10 1.040829795858E+01 -1.477498160536E+00 -1.056169984492E+01 154 ib 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 155 db 10 7.803585070708E-02 -7.881841344928E-02 5.961861704021E-02 156 tot 10 1.048633380929E+01 -1.556316573985E+00 -1.050208122788E+01 157 qf 11 1.886612704424E+00 -2.155915536500E+00 3.653356391714E+00 158 ib 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 159 db 11 -5.379874191468E-02 3.656434367407E-02 -3.874817966881E-02 160 tot 11 1.832813962509E+00 -2.119351192826E+00 3.614608212045E+00 161 qf 12 -4.589758090567E+00 -5.985997827646E+00 -2.262135898805E+00 162 ib 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 163 db 12 4.713429967783E-01 3.555339814866E-01 3.630350857632E-01 164 tot 12 -4.118415093788E+00 -5.630463846160E+00 -1.899100813042E+00 165 qf 13 -2.178337475994E+00 7.837800424267E-01 6.699601634927E-01 166 ib 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 167 db 13 8.437945422216E-02 -6.730905540050E-01 1.679489122962E-01 168 tot 13 -2.093958021772E+00 1.106894884217E-01 8.379090757888E-01 169 qf 14 -3.478917654185E+00 3.274531596988E+01 8.826058570314E+01 170 ib 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 171 db 14 -3.211275274981E-01 1.449884122095E-01 1.484963357034E-01 172 tot 14 -3.800045181683E+00 3.289030438209E+01 8.840908203884E+01 173 qf 15 1.136014888745E+02 -1.824151429142E+02 9.157163006266E+01 174 ib 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 175 db 15 -3.773072304527E+00 2.815398569426E-01 -1.102074587349E-02 176 tot 15 1.098284165699E+02 -1.821336030572E+02 9.156060931678E+01 177 qf 16 3.584635943075E+01 -8.556117773390E+01 4.632179727081E+01 178 ib 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 179 db 16 2.707625367578E+00 -1.087607703804E+00 1.833388674637E-01 180 tot 16 3.855398479833E+01 -8.664878543770E+01 4.650513613827E+01 181 qf 17 -3.128648152641E+01 4.903088438960E+01 1.832384450185E+01 182 ib 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 183 db 17 1.245177643423E-01 -4.822564750973E-02 -7.875600562191E-03 184 tot 17 -3.116196376207E+01 4.898265874209E+01 1.831596890129E+01 185 qf 18 8.713235777586E+00 1.714284629384E+01 6.445699283183E+00 186 ib 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 187 db 18 -9.131631309058E-02 2.587722524915E-03 5.780803000813E-03 188 tot 18 8.621919464496E+00 1.714543401637E+01 6.451480086184E+00 189 qf 19 3.647949487435E+00 -1.004992529255E+01 2.106345970750E+00 190 ib 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 191 db 19 -6.381310633539E-01 -2.750669343433E-03 2.419154933592E-03 192 tot 19 3.009818424081E+00 -1.005267596190E+01 2.108765125683E+00 193 qf 20 -5.748601577339E+00 -7.560561256258E+00 -4.799757889654E+00 194 ib 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 195 db 20 3.557735298313E-02 6.150668525524E-02 1.350188563218E-01 196 tot 20 -5.713024224356E+00 -7.499054571002E+00 -4.664739033332E+00 197 qf 21 -5.657437325902E+00 -7.248744005541E+00 5.737056824424E+00 198 ib 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 199 db 21 3.430523651614E-02 6.097777255684E-02 -1.362183049517E-01 200 tot 21 -5.623132089386E+00 -7.187766232984E+00 5.600838519473E+00 201 tot all -6.368452708591E+01 -1.767437750376E+02 5.224722160544E+02 202 203print APOL force 1 (npolar) end 204 Printing per atom forces (kJ/mol/A) 205 Legend: 206 tot n -- Total force for atom n 207 sasa n -- SASA force for atom n 208 sav n -- SAV force for atom n 209 wca n -- WCA force for atom n 210 tot all -- Total force for system 211 sasa 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00 212 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 213 wca 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 214 tot 0 -1.053397375968E+01 -2.467959566553E+01 0.000000000000E+00 215 sasa 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00 216 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 217 wca 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 218 tot 1 -2.331383043616E+01 -1.778173507843E+01 0.000000000000E+00 219 sasa 2 -1.881066742799E+01 -6.019413576958E-01 1.926212344627E+01 220 sav 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 221 wca 2 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 222 tot 2 -1.881066742799E+01 -6.019413576958E-01 1.926212344627E+01 223 sasa 3 -1.941260878569E+01 -1.655338733663E+00 -1.775727005203E+01 224 sav 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 225 wca 3 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 226 tot 3 -1.941260878569E+01 -1.655338733663E+00 -1.775727005203E+01 227 sasa 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00 228 sav 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 229 wca 4 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 230 tot 4 2.370898010457E+00 -5.729670191939E+00 7.310268865577E+00 231 sasa 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00 232 sav 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 233 wca 5 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 234 tot 5 9.644037477214E+00 -1.844210675467E+01 4.568228278680E+00 235 sasa 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00 236 sav 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 237 wca 6 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 238 tot 6 -9.383410046471E+00 7.694396238106E+00 7.319059836247E+00 239 sasa 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 240 sav 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 241 wca 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 242 tot 7 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 243 sasa 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00 244 sav 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 245 wca 8 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 246 tot 8 -1.778173507843E+00 5.927245026143E-01 7.112694031372E+00 247 sasa 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01 248 sav 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 249 wca 9 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 250 tot 9 6.310838634859E+00 -1.682890302629E+00 1.795082989471E+01 251 sasa 10 2.410412977298E+01 -1.106419071547E+01 -2.133808209412E+01 252 sav 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 253 wca 10 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 254 tot 10 2.410412977298E+01 -1.106419071547E+01 -2.133808209412E+01 255 sasa 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01 256 sav 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 257 wca 11 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 258 tot 11 1.655338733663E+00 -9.029120365437E-01 -2.467959566553E+01 259 sasa 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00 260 sav 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 261 wca 12 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 262 tot 12 2.437862498668E+01 -3.310677467327E+00 -9.029120365437E+00 263 sasa 13 1.850969674915E+01 -1.610193131836E+01 -1.143688579622E+01 264 sav 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 265 wca 13 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 266 tot 13 1.850969674915E+01 -1.610193131836E+01 -1.143688579622E+01 267 sasa 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01 268 sav 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 269 wca 14 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 270 tot 14 -3.161197347277E+00 4.346646352505E+00 1.066904104706E+01 271 sasa 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00 272 sav 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 273 wca 15 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 274 tot 15 -1.894968767453E+01 9.136456557360E+00 3.553066438974E+00 275 sasa 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00 276 sav 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 277 wca 16 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 278 tot 16 1.651480168179E+01 -1.501345607435E+00 7.506728037177E+00 279 sasa 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 280 sav 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 281 wca 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 282 tot 17 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 283 sasa 18 4.346646352505E+00 4.267616418823E+01 3.951496684096E-01 284 sav 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 285 wca 18 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 286 tot 18 4.346646352505E+00 4.267616418823E+01 3.951496684096E-01 287 sasa 19 -1.654842130919E+01 2.468239110523E+01 0.000000000000E+00 288 sav 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 289 wca 19 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 290 tot 19 -1.654842130919E+01 2.468239110523E+01 0.000000000000E+00 291 sasa 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01 292 sav 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 293 wca 20 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 294 tot 20 1.220095469406E+01 1.753010731905E+01 2.131661049997E+01 295 sasa 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01 296 sav 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 297 wca 21 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 298 tot 21 1.192047297696E+01 1.823131161181E+01 -2.005444277300E+01 299 tot all 1.006446977549E+01 2.143586264522E+01 2.668403298113E+00 300 301print energy 1 (elec) end 302 Local net energy (PE 0) = 1.089755873935E+03 kJ/mol 303 Global net ELEC energy = 1.089755873935E+03 kJ/mol 304 305print APOL energy 1 (npolar) end 306 Global net APOL energy = 4.148317453106E+01 kJ/mol 307---------------------------------------- 308CLEANING UP AND SHUTTING DOWN... 309Final memory usage: 8.454 MB total, 8.667 MB high water 310 311 312Thanks for using APBS! 313 314