1
2          -------------------------------------------------------
3          Amber 9  SANDER                              2006
4          -------------------------------------------------------
5
6| Run on 09/24/2007 at 22:04:50
7  [-O]verwriting output
8
9File Assignments:
10|  MDIN: solvation.in
11| MDOUT: Ba
12|INPCRD: 2ala.prmcrd
13|  PARM: 2ala.prmtop
14|RESTRT: restrt
15|  REFC: refc
16| MDVEL: mdvel
17|  MDEN: mden
18| MDCRD: mdcrd
19|MDINFO: mdinfo
20|INPDIP: inpdip
21|RSTDIP: rstdip
22
23
24 Here is the input file:
25
26APBS solvation energy example
27&cntrl
28   maxcyc=0, imin=1,
29   cut=12.0,
30   igb=6, ntb=0,
31   ntpr=1,
32 /
33&apbs
34    apbs_debug=9,
35    apbs_print=1,
36    grid=0.5, 0.5, 0.5,
37    calc_type=0,
38    cmeth=1,
39 bcfl=2,
40 srfm=1,
41 chgm=1,
42 pdie=1.0,
43 sdie=78.54,
44 srad = 1.4,
45 radiopt=3, pqr='2ala.pqr',
46 calcforce=0, calcnpenergy=1,
47&end
48
49--------------------------------------------------------------------------------
50   1.  RESOURCE   USE:
51--------------------------------------------------------------------------------
52
53| Flags:
54| New format PARM file being parsed.
55| Version =    1.000 Date = 10/18/06 Time = 21:21:36
56 NATOM  =      22 NTYPES =       7 NBONH =      12 MBONA  =       9
57 NTHETH =      25 MTHETA =      11 NPHIH =      42 MPHIA  =      18
58 NHPARM =       0 NPARM  =       0 NNB   =      99 NRES   =       3
59 NBONA  =       9 NTHETA =      11 NPHIA =      18 NUMBND =       8
60 NUMANG =      16 NPTRA  =      16 NATYP =       7 NPHB   =       0
61 IFBOX  =       0 NMXRS  =      10 IFCAP =       0 NEXTRA =       0
62 NCOPY  =       0
63
64 Implicit solvent radii are modified Bondi radii (mbondi)
65
66|     Memory Use     Allocated
67|     Real                1592
68|     Hollerith            137
69|     Integer            21004
70|     Max Pairs              1
71|     nblistReal             0
72|     nblist Int             0
73|       Total               95 kbytes
74| Duplicated    0 dihedrals
75| Duplicated    0 dihedrals
76
77--------------------------------------------------------------------------------
78   2.  CONTROL  DATA  FOR  THE  RUN
79--------------------------------------------------------------------------------
80
81ACE
82
83General flags:
84     imin    =       1, nmropt  =       0
85
86Nature and format of input:
87     ntx     =       1, irest   =       0, ntrx    =       1
88
89Nature and format of output:
90     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
91     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
92     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0
93
94Potential function:
95     ntf     =       1, ntb     =       0, igb     =       6, nsnb    =      25
96     ipol    =       0, gbsa    =       0, iesp    =       0
97     dielc   =   1.00000, cut     =  12.00000, intdiel =   1.00000
98     saltcon =   0.00000, offset  =   0.09000, gbalpha=    1.00000
99     gbbeta  =   0.00000, gbgamma =   0.00000, surften =   0.00500
100     rdt     =   0.00000, rgbmax  =  25.00000
101     alpb  =        0
102     scnb    =   2.00000, scee    =   1.20000
103
104Frozen or restrained atoms:
105     ibelly  =       0, ntr     =       0
106
107Energy minimization:
108     maxcyc  =       0, ncyc    =      10, ntmin   =       1
109     dx0     =   0.01000, drms    =   0.00010
110|  INFO: Old style inpcrd file read
111
112
113--------------------------------------------------------------------------------
114   3.  ATOMIC COORDINATES AND VELOCITIES
115--------------------------------------------------------------------------------
116
117ACE
118 begin time read from input coords =     0.000 ps
119
120iAPBS: Initializing APBS interface
121iAPBS: Reading radii definition from pqr filename: 2ala.pqr
122iAPBS: Grid dime not specified, calculating ...
123iAPBS: Requesting recalculating dime during caclulations.
124iAPBS: Grid values:
125fglen:   13.801  18.154  10.192
126cglen:   13.801  18.154  10.192
127dime:   33  33  33
128grid:    0.500   0.500   0.500
129Required memory (in MB):      6.854
130
131 APBS calculation parameters:
132
133Nonlinear traditional PBE
134Multiple Debye-Huckel boundary conditions
135Smoothed molecular surface definition.
136Using cubic B-spline discretization
137Grid dimension:  33  33  33
138Coarse grid lengths:  13.801  18.154  10.192
139Fine grid lengths:  13.801  18.154  10.192
140Grid spacings:   0.500   0.500   0.500
141Solute dielectric (pdie):   1.000
142Solvent dielectric (sdie):  78.540
143Temperature: 298.150
144Surface sphere density (sdens):  10.000
145Surface tension:   0.105
146radiopt is set to 3
147
148 Number of triangulated 3-point waters found:        0
149
150--------------------------------------------------------------------------------
151   4.  RESULTS
152--------------------------------------------------------------------------------
153
154iAPBS: unpacked coordinates, charge and radius:
155   1   2.000   1.000   0.000   0.112   1.487
156   2   2.000   2.090   0.000  -0.366   1.908
157   3   1.486   2.454   0.890   0.112   1.487
158   4   1.486   2.454  -0.890   0.112   1.487
159   5   3.427   2.641   0.000   0.597   1.908
160   6   4.391   1.877   0.000  -0.568   1.661
161   7   3.555   3.970   0.000  -0.416   1.824
162   8   2.733   4.556   0.000   0.272   0.600
163   9   4.853   4.614   0.000   0.034   1.908
164  10   5.408   4.316   0.890   0.082   1.387
165  11   5.661   4.221  -1.232  -0.182   1.908
166  12   5.123   4.521  -2.131   0.060   1.487
167  13   6.630   4.719  -1.206   0.060   1.487
168  14   5.809   3.141  -1.241   0.060   1.487
169  15   4.713   6.129   0.000   0.597   1.908
170  16   3.601   6.653   0.000  -0.568   1.661
171  17   5.846   6.835   0.000  -0.416   1.824
172  18   6.737   6.359   0.000   0.272   0.600
173  19   5.846   8.284   0.000  -0.149   1.908
174  20   4.819   8.648   0.000   0.098   1.387
175  21   6.360   8.648   0.890   0.098   1.387
176  22   6.360   8.648  -0.890   0.098   1.387
177iAPBS: Calling apbsdrv
178iAPBS: apbs return code:            0
179iAPBS: apbs return code:            0
180iAPBS: TotalForces:       1   4.108   0.761  -0.017
181iAPBS: TotalForces:       2   6.437   8.400   0.055
182iAPBS: TotalForces:       3   0.126  -1.054  -1.019
183iAPBS: TotalForces:       4   0.162  -1.035   0.979
184iAPBS: TotalForces:       5 -10.816  -5.205   3.291
185iAPBS: TotalForces:       6 -15.856  -9.593   9.277
186iAPBS: TotalForces:       7  -1.998 -18.943  -5.755
187iAPBS: TotalForces:       8   1.173   1.094  -0.176
188iAPBS: TotalForces:       9   8.610   9.436   1.432
189iAPBS: TotalForces:      10  -0.417  -0.207   1.012
190iAPBS: TotalForces:      11   0.958  -4.145  -7.140
191iAPBS: TotalForces:      12   0.424  -0.661  -1.502
192iAPBS: TotalForces:      13   1.974  -4.806  -3.120
193iAPBS: TotalForces:      14   9.767   6.261  -7.979
194iAPBS: TotalForces:      15  -1.239   0.475   7.502
195iAPBS: TotalForces:      16  -5.177  -1.051  -0.431
196iAPBS: TotalForces:      17  -1.541   8.188   3.810
197iAPBS: TotalForces:      18  -3.350  -2.477  -0.165
198iAPBS: TotalForces:      19   6.599   4.841  -0.004
199iAPBS: TotalForces:      20   0.937   6.805  -0.022
200iAPBS: TotalForces:      21  -0.437   1.472   0.515
201iAPBS: TotalForces:      22  -0.447   1.444  -0.543
202iAPBS: SolventForces:     1   0.000   0.000   0.000
203iAPBS: SolventForces:     2   0.000   0.000   0.000
204iAPBS: SolventForces:     3   0.000   0.000   0.000
205iAPBS: SolventForces:     4   0.000   0.000   0.000
206iAPBS: SolventForces:     5   0.000   0.000   0.000
207iAPBS: SolventForces:     6   0.000   0.000   0.000
208iAPBS: SolventForces:     7   0.000   0.000   0.000
209iAPBS: SolventForces:     8   0.000   0.000   0.000
210iAPBS: SolventForces:     9   0.000   0.000   0.000
211iAPBS: SolventForces:    10   0.000   0.000   0.000
212iAPBS: SolventForces:    11   0.000   0.000   0.000
213iAPBS: SolventForces:    12   0.000   0.000   0.000
214iAPBS: SolventForces:    13   0.000   0.000   0.000
215iAPBS: SolventForces:    14   0.000   0.000   0.000
216iAPBS: SolventForces:    15   0.000   0.000   0.000
217iAPBS: SolventForces:    16   0.000   0.000   0.000
218iAPBS: SolventForces:    17   0.000   0.000   0.000
219iAPBS: SolventForces:    18   0.000   0.000   0.000
220iAPBS: SolventForces:    19   0.000   0.000   0.000
221iAPBS: SolventForces:    20   0.000   0.000   0.000
222iAPBS: SolventForces:    21   0.000   0.000   0.000
223iAPBS: SolventForces:    22   0.000   0.000   0.000
224iAPBS: VacuumForces:      1   0.000   0.000   0.000
225iAPBS: VacuumForces:      2   0.000   0.000   0.000
226iAPBS: VacuumForces:      3   0.000   0.000   0.000
227iAPBS: VacuumForces:      4   0.000   0.000   0.000
228iAPBS: VacuumForces:      5   0.000   0.000   0.000
229iAPBS: VacuumForces:      6   0.000   0.000   0.000
230iAPBS: VacuumForces:      7   0.000   0.000   0.000
231iAPBS: VacuumForces:      8   0.000   0.000   0.000
232iAPBS: VacuumForces:      9   0.000   0.000   0.000
233iAPBS: VacuumForces:     10   0.000   0.000   0.000
234iAPBS: VacuumForces:     11   0.000   0.000   0.000
235iAPBS: VacuumForces:     12   0.000   0.000   0.000
236iAPBS: VacuumForces:     13   0.000   0.000   0.000
237iAPBS: VacuumForces:     14   0.000   0.000   0.000
238iAPBS: VacuumForces:     15   0.000   0.000   0.000
239iAPBS: VacuumForces:     16   0.000   0.000   0.000
240iAPBS: VacuumForces:     17   0.000   0.000   0.000
241iAPBS: VacuumForces:     18   0.000   0.000   0.000
242iAPBS: VacuumForces:     19   0.000   0.000   0.000
243iAPBS: VacuumForces:     20   0.000   0.000   0.000
244iAPBS: VacuumForces:     21   0.000   0.000   0.000
245iAPBS: VacuumForces:     22   0.000   0.000   0.000
246iAPBS: SolvForces:        1   0.000   0.000   0.000
247iAPBS: SolvForces:        2   0.000   0.000   0.000
248iAPBS: SolvForces:        3   0.000   0.000   0.000
249iAPBS: SolvForces:        4   0.000   0.000   0.000
250iAPBS: SolvForces:        5   0.000   0.000   0.000
251iAPBS: SolvForces:        6   0.000   0.000   0.000
252iAPBS: SolvForces:        7   0.000   0.000   0.000
253iAPBS: SolvForces:        8   0.000   0.000   0.000
254iAPBS: SolvForces:        9   0.000   0.000   0.000
255iAPBS: SolvForces:       10   0.000   0.000   0.000
256iAPBS: SolvForces:       11   0.000   0.000   0.000
257iAPBS: SolvForces:       12   0.000   0.000   0.000
258iAPBS: SolvForces:       13   0.000   0.000   0.000
259iAPBS: SolvForces:       14   0.000   0.000   0.000
260iAPBS: SolvForces:       15   0.000   0.000   0.000
261iAPBS: SolvForces:       16   0.000   0.000   0.000
262iAPBS: SolvForces:       17   0.000   0.000   0.000
263iAPBS: SolvForces:       18   0.000   0.000   0.000
264iAPBS: SolvForces:       19   0.000   0.000   0.000
265iAPBS: SolvForces:       20   0.000   0.000   0.000
266iAPBS: SolvForces:       21   0.000   0.000   0.000
267iAPBS: SolvForces:       22   0.000   0.000   0.000
268iAPBS: qfForces:          1   0.000   0.000   0.000
269iAPBS: qfForces:          2   0.000   0.000   0.000
270iAPBS: qfForces:          3   0.000   0.000   0.000
271iAPBS: qfForces:          4   0.000   0.000   0.000
272iAPBS: qfForces:          5   0.000   0.000   0.000
273iAPBS: qfForces:          6   0.000   0.000   0.000
274iAPBS: qfForces:          7   0.000   0.000   0.000
275iAPBS: qfForces:          8   0.000   0.000   0.000
276iAPBS: qfForces:          9   0.000   0.000   0.000
277iAPBS: qfForces:         10   0.000   0.000   0.000
278iAPBS: qfForces:         11   0.000   0.000   0.000
279iAPBS: qfForces:         12   0.000   0.000   0.000
280iAPBS: qfForces:         13   0.000   0.000   0.000
281iAPBS: qfForces:         14   0.000   0.000   0.000
282iAPBS: qfForces:         15   0.000   0.000   0.000
283iAPBS: qfForces:         16   0.000   0.000   0.000
284iAPBS: qfForces:         17   0.000   0.000   0.000
285iAPBS: qfForces:         18   0.000   0.000   0.000
286iAPBS: qfForces:         19   0.000   0.000   0.000
287iAPBS: qfForces:         20   0.000   0.000   0.000
288iAPBS: qfForces:         21   0.000   0.000   0.000
289iAPBS: qfForces:         22   0.000   0.000   0.000
290iAPBS: ibForces:          1   0.000   0.000   0.000
291iAPBS: ibForces:          2   0.000   0.000   0.000
292iAPBS: ibForces:          3   0.000   0.000   0.000
293iAPBS: ibForces:          4   0.000   0.000   0.000
294iAPBS: ibForces:          5   0.000   0.000   0.000
295iAPBS: ibForces:          6   0.000   0.000   0.000
296iAPBS: ibForces:          7   0.000   0.000   0.000
297iAPBS: ibForces:          8   0.000   0.000   0.000
298iAPBS: ibForces:          9   0.000   0.000   0.000
299iAPBS: ibForces:         10   0.000   0.000   0.000
300iAPBS: ibForces:         11   0.000   0.000   0.000
301iAPBS: ibForces:         12   0.000   0.000   0.000
302iAPBS: ibForces:         13   0.000   0.000   0.000
303iAPBS: ibForces:         14   0.000   0.000   0.000
304iAPBS: ibForces:         15   0.000   0.000   0.000
305iAPBS: ibForces:         16   0.000   0.000   0.000
306iAPBS: ibForces:         17   0.000   0.000   0.000
307iAPBS: ibForces:         18   0.000   0.000   0.000
308iAPBS: ibForces:         19   0.000   0.000   0.000
309iAPBS: ibForces:         20   0.000   0.000   0.000
310iAPBS: ibForces:         21   0.000   0.000   0.000
311iAPBS: ibForces:         22   0.000   0.000   0.000
312iAPBS: npForces:          1   0.000   0.000   0.000
313iAPBS: npForces:          2   0.000   0.000   0.000
314iAPBS: npForces:          3   0.000   0.000   0.000
315iAPBS: npForces:          4   0.000   0.000   0.000
316iAPBS: npForces:          5   0.000   0.000   0.000
317iAPBS: npForces:          6   0.000   0.000   0.000
318iAPBS: npForces:          7   0.000   0.000   0.000
319iAPBS: npForces:          8   0.000   0.000   0.000
320iAPBS: npForces:          9   0.000   0.000   0.000
321iAPBS: npForces:         10   0.000   0.000   0.000
322iAPBS: npForces:         11   0.000   0.000   0.000
323iAPBS: npForces:         12   0.000   0.000   0.000
324iAPBS: npForces:         13   0.000   0.000   0.000
325iAPBS: npForces:         14   0.000   0.000   0.000
326iAPBS: npForces:         15   0.000   0.000   0.000
327iAPBS: npForces:         16   0.000   0.000   0.000
328iAPBS: npForces:         17   0.000   0.000   0.000
329iAPBS: npForces:         18   0.000   0.000   0.000
330iAPBS: npForces:         19   0.000   0.000   0.000
331iAPBS: npForces:         20   0.000   0.000   0.000
332iAPBS: npForces:         21   0.000   0.000   0.000
333iAPBS: npForces:         22   0.000   0.000   0.000
334iAPBS: dbForces:          1   0.000   0.000   0.000
335iAPBS: dbForces:          2   0.000   0.000   0.000
336iAPBS: dbForces:          3   0.000   0.000   0.000
337iAPBS: dbForces:          4   0.000   0.000   0.000
338iAPBS: dbForces:          5   0.000   0.000   0.000
339iAPBS: dbForces:          6   0.000   0.000   0.000
340iAPBS: dbForces:          7   0.000   0.000   0.000
341iAPBS: dbForces:          8   0.000   0.000   0.000
342iAPBS: dbForces:          9   0.000   0.000   0.000
343iAPBS: dbForces:         10   0.000   0.000   0.000
344iAPBS: dbForces:         11   0.000   0.000   0.000
345iAPBS: dbForces:         12   0.000   0.000   0.000
346iAPBS: dbForces:         13   0.000   0.000   0.000
347iAPBS: dbForces:         14   0.000   0.000   0.000
348iAPBS: dbForces:         15   0.000   0.000   0.000
349iAPBS: dbForces:         16   0.000   0.000   0.000
350iAPBS: dbForces:         17   0.000   0.000   0.000
351iAPBS: dbForces:         18   0.000   0.000   0.000
352iAPBS: dbForces:         19   0.000   0.000   0.000
353iAPBS: dbForces:         20   0.000   0.000   0.000
354iAPBS: dbForces:         21   0.000   0.000   0.000
355iAPBS: dbForces:         22   0.000   0.000   0.000
356
357
358   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
359      1      -1.9290E+01     5.3610E+00     1.8943E+01     N           7
360
361 BOND    =        0.0206  ANGLE   =        0.3620  DIHED      =        8.1071
362 VDWAALS =        2.8120  EEL     =      -80.1238  EPB        =      -14.3348
363 1-4 VDW =        5.0157  1-4 EEL =       48.9355  RESTRAINT  =        0.0000
364 ENPOLAR =        9.9161
365
366
367  Maximum number of minimization cycles reached.
368
369
370                    FINAL RESULTS
371
372
373
374   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
375      1      -1.9290E+01     5.3610E+00     1.8943E+01     N           7
376
377 BOND    =        0.0206  ANGLE   =        0.3620  DIHED      =        8.1071
378 VDWAALS =        2.8120  EEL     =      -80.1238  EPB        =      -14.3348
379 1-4 VDW =        5.0157  1-4 EEL =       48.9355  RESTRAINT  =        0.0000
380 ENPOLAR =        9.9161
381
382--------------------------------------------------------------------------------
383   5.  TIMINGS
384--------------------------------------------------------------------------------
385
386|    Read coords time           0.00 ( 0.06% of Total)
387|             PB Nonbond                 0.88 (100.0% of Nonbo)
388|          Nonbond force              0.88 (100.0% of Force)
389|          Bond/Angle/Dihedral        0.00 ( 0.01% of Force)
390|       Force time                 0.88 (100.0% of Runmd)
391|    Runmd Time                 0.88 (99.69% of Total)
392|    Other                      0.00 ( 0.25% of Total)
393| Total time                 0.88 (100.0% of ALL  )
394
395| Highest rstack allocated:          0
396| Highest istack allocated:          0
397|           Job began  at 22:04:50.491  on 09/24/2007
398|           Setup done at 22:04:50.494  on 09/24/2007
399|           Run   done at 22:04:51.373  on 09/24/2007
400|     wallclock() was called      22 times
401