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