1
2          -------------------------------------------------------
3          Amber 9  SANDER                              2006
4          -------------------------------------------------------
5
6| Run on 09/24/2007 at 15:22:46
7  [-O]verwriting output
8
9File Assignments:
10|  MDIN: iapbs.in
11| MDOUT: iapbs.3.parse.out
12|INPCRD: pgb.rst
13|  PARM: 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
26 test of PB reaction field on protein g solvated in a sphere (iAPBS)
27&cntrl
28   ntx=1, irest=0,
29   imin=1, ntmin=2, maxcyc=0,
30   ntpr=1, igb=6, ntb=0,
31   ntc=1, ntf=1, tol=0.000001,
32 /
33&apbs
34    apbs_debug=0, apbs_print=1,
35    grid = 0.5, 0.5, 0.5,
36    calc_type=0,     cmeth=1,
37 bcfl=2, srfm=0,
38 chgm=0, srad =1.4, swin =0.3,
39 pdie=1.0,  sdie=80.0,
40 calcforce=0,
41 radiopt=3, pqr='pgb-parse.pqr',
42&end
43
44--------------------------------------------------------------------------------
45   1.  RESOURCE   USE:
46--------------------------------------------------------------------------------
47
48| Flags:
49| New format PARM file being parsed.
50| Version =    1.000 Date = 03/08/04 Time = 15:34:25
51 NATOM  =     855 NTYPES =      13 NBONH =     419 MBONA  =     442
52 NTHETH =     951 MTHETA =     600 NPHIH =    1716 MPHIA  =    1040
53 NHPARM =       0 NPARM  =       0 NNB   =    4698 NRES   =      56
54 NBONA  =     442 NTHETA =     600 NPHIA =    1040 NUMBND =      30
55 NUMANG =      65 NPTRA  =      26 NATYP =      21 NPHB   =       0
56 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
57 NCOPY  =       0
58
59
60|     Memory Use     Allocated
61|     Real               55051
62|     Hollerith           5188
63|     Integer            61665
64|     Max Pairs              1
65|     nblistReal             0
66|     nblist Int             0
67|       Total              691 kbytes
68| Duplicated    0 dihedrals
69| Duplicated    0 dihedrals
70
71--------------------------------------------------------------------------------
72   2.  CONTROL  DATA  FOR  THE  RUN
73--------------------------------------------------------------------------------
74
75
76
77General flags:
78     imin    =       1, nmropt  =       0
79
80Nature and format of input:
81     ntx     =       1, irest   =       0, ntrx    =       1
82
83Nature and format of output:
84     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
85     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
86     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0
87
88Potential function:
89     ntf     =       1, ntb     =       0, igb     =       6, nsnb    =      25
90     ipol    =       0, gbsa    =       0, iesp    =       0
91     dielc   =   1.00000, cut     =   8.00000, intdiel =   1.00000
92     saltcon =   0.00000, offset  =   0.09000, gbalpha=    1.00000
93     gbbeta  =   0.00000, gbgamma =   0.00000, surften =   0.00500
94     rdt     =   0.00000, rgbmax  =  25.00000
95     alpb  =        0
96     scnb    =   2.00000, scee    =   1.20000
97
98Frozen or restrained atoms:
99     ibelly  =       0, ntr     =       0
100
101Energy minimization:
102     maxcyc  =       0, ncyc    =      10, ntmin   =       2
103     dx0     =   0.01000, drms    =   0.00010
104|  INFO: Old style inpcrd file read
105
106
107--------------------------------------------------------------------------------
108   3.  ATOMIC COORDINATES AND VELOCITIES
109--------------------------------------------------------------------------------
110
111
112 begin time read from input coords =     0.000 ps
113
114iAPBS: Initializing APBS interface
115iAPBS: Reading radii definition from pqr filename: pgb-parse.pqr
116iAPBS: Grid dime not specified, calculating ...
117iAPBS: Requesting recalculating dime during caclulations.
118iAPBS: Grid values:
119fglen:   39.487  53.381  51.722
120cglen:   39.487  56.747  53.927
121dime:   65  97  97
122grid:    0.500   0.500   0.500
123Required memory (in MB):    116.651
124
125 APBS calculation parameters:
126
127Nonlinear traditional PBE
128Multiple Debye-Huckel boundary conditions
129Molecular surface definition
130Using trilinear interpolation (linear splines)
131Grid dimension:  65  97  97
132Coarse grid lengths:  39.487  56.747  53.927
133Fine grid lengths:  39.487  53.381  51.722
134Grid spacings:   0.500   0.500   0.500
135Solute dielectric (pdie):   1.000
136Solvent dielectric (sdie):  80.000
137Temperature: 298.150
138sdens:  10.000
139Surface tension:   0.105
140radiopt is set to 3
141
142 Number of triangulated 3-point waters found:        0
143
144--------------------------------------------------------------------------------
145   4.  RESULTS
146--------------------------------------------------------------------------------
147
148
149
150   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
151      1      -2.3064E+03     2.8943E+00     2.2881E+01     CG        606
152
153 BOND    =       15.9232  ANGLE   =       72.0306  DIHED      =      259.6946
154 VDWAALS =     -400.2516  EEL     =    -4454.9764  EPB        =    -1132.0474
155 1-4 VDW =      182.2148  1-4 EEL =     3058.2617  RESTRAINT  =        0.0000
156 ENPOLAR =       92.7357
157
158
159  Maximum number of minimization cycles reached.
160
161
162                    FINAL RESULTS
163
164
165
166   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
167      1      -2.3064E+03     2.8943E+00     2.2881E+01     CG        606
168
169 BOND    =       15.9232  ANGLE   =       72.0306  DIHED      =      259.6946
170 VDWAALS =     -400.2516  EEL     =    -4454.9764  EPB        =    -1132.0474
171 1-4 VDW =      182.2148  1-4 EEL =     3058.2617  RESTRAINT  =        0.0000
172 ENPOLAR =       92.7357
173
174--------------------------------------------------------------------------------
175   5.  TIMINGS
176--------------------------------------------------------------------------------
177
178|    Read coords time           0.00 ( 0.02% of Total)
179|                Calc gb off-diag           0.01 (99.85% of Gen B)
180|                Other                      0.00 ( 0.15% of Gen B)
181|             Gen Born time              0.01 ( 0.02% of Nonbo)
182|             PB Nonbond                23.68 (100.0% of Nonbo)
183|          Nonbond force             23.69 (100.0% of Force)
184|       Force time                23.69 (100.0% of Runmd)
185|    Runmd Time                23.69 (100.0% of Total)
186|    Other                      0.01 ( 0.06% of Total)
187| Total time                23.71 (100.0% of ALL  )
188
189| Highest rstack allocated:          0
190| Highest istack allocated:          0
191|           Job began  at 15:22:46.772  on 09/24/2007
192|           Setup done at 15:22:46.787  on 09/24/2007
193|           Run   done at 15:23:10.479  on 09/24/2007
194|     wallclock() was called      22 times
195