1
2          -------------------------------------------------------
3          Amber 10 SANDER                              2008
4          -------------------------------------------------------
5
6| Run on 05/28/2008 at 14:02:46
7  [-O]verwriting output
8
9File Assignments:
10|  MDIN: mdin
11| MDOUT: lyn.out
12|INPCRD: ./prmtop-inpcrd/lyn.inpcrd
13|  PARM: ./prmtop-inpcrd/lyn.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 iAPBS/sander solvation energies (based on pbsa_radi)
27 &cntrl
28   ntx=1, irest=0,
29   imin=1, maxcyc=0,
30   ntpr=1, ntwr=100000,
31   igb=6, ntb=0,
32   ntc=1, ntf=1, tol=0.000001,
33   ntt=0, temp0=300
34 &end
35 &apbs
36    apbs_debug=0,
37    apbs_print=0,
38    grid=0.5, 0.5, 0.5,
39    calc_type=0,
40    cmeth=1,
41    bcfl=2,
42    srfm=1,
43    chgm=1,
44    pdie=1.0,
45    sdie=80.0,
46    srad = 1.4,
47    radiopt=0,
48    calcforce=0, calcnpenergy=1,
49&end
50
51--------------------------------------------------------------------------------
52   1.  RESOURCE   USE:
53--------------------------------------------------------------------------------
54
55| Flags:
56| New format PARM file being parsed.
57| Version =    1.000 Date = 01/07/05 Time = 17:56:14
58 NATOM  =      16 NTYPES =       5 NBONH =      11 MBONA  =       4
59 NTHETH =      24 MTHETA =       3 NPHIH =      31 MPHIA  =       4
60 NHPARM =       0 NPARM  =       0 NNB   =      77 NRES   =       1
61 NBONA  =       4 NTHETA =       3 NPHIA =       4 NUMBND =       5
62 NUMANG =       9 NPTRA  =       6 NATYP =       5 NPHB   =       0
63 IFBOX  =       0 NMXRS  =      16 IFCAP =       0 NEXTRA =       0
64 NCOPY  =       0
65
66
67|     Memory Use     Allocated
68|     Real                1182
69|     Hollerith             99
70|     Integer            20687
71|     Max Pairs              1
72|     nblistReal             0
73|     nblist Int             0
74|       Total               90 kbytes
75| Duplicated    0 dihedrals
76| Duplicated    0 dihedrals
77
78--------------------------------------------------------------------------------
79   2.  CONTROL  DATA  FOR  THE  RUN
80--------------------------------------------------------------------------------
81
82LYN
83
84General flags:
85     imin    =       1, nmropt  =       0
86
87Nature and format of input:
88     ntx     =       1, irest   =       0, ntrx    =       1
89
90Nature and format of output:
91     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =  100000
92     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
93     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0
94
95Potential function:
96     ntf     =       1, ntb     =       0, igb     =       6, nsnb    =      25
97     ipol    =       0, gbsa    =       0, iesp    =       0
98     dielc   =   1.00000, cut     =   8.00000, intdiel =   1.00000
99     saltcon =   0.00000, offset  =   0.09000, gbalpha=    1.00000
100     gbbeta  =   0.00000, gbgamma =   0.00000, surften =   0.00500
101     rdt     =   0.00000, rgbmax  =  25.00000  extdiel =  78.50000
102     alpb  =        0
103     scnb    =   2.00000, scee    =   1.20000
104
105Frozen or restrained atoms:
106     ibelly  =       0, ntr     =       0
107
108Energy minimization:
109     maxcyc  =       0, ncyc    =      10, ntmin   =       1
110     dx0     =   0.01000, drms    =   0.00010
111|  INFO: Old style inpcrd file read
112
113
114--------------------------------------------------------------------------------
115   3.  ATOMIC COORDINATES AND VELOCITIES
116--------------------------------------------------------------------------------
117
118LYN
119 begin time read from input coords =     0.000 ps
120
121iAPBS: Initializing APBS interface
122iAPBS: Using charge/radii definition from prmtop file
123iAPBS: Grid dime not specified, calculating ...
124iAPBS: Requesting dime re-calculation on the fly
125
126 APBS calculation parameters:
127
128Nonlinear traditional PBE
129Multiple Debye-Huckel boundary conditions
130Smoothed molecular surface definition
131Using cubic B-spline discretization
132Grid dimension:  33  33  33
133Coarse grid lengths:   9.794  14.169  10.423 A
134Fine grid lengths:   9.794  14.169  10.423 A
135Grid spacings:   0.500   0.500   0.500 A
136Solute dielectric (pdie):   1.000
137Solvent dielectric (sdie):  80.000
138Temperature: 298.150 K
139Surface sphere density (sdens):  10.000 grid points/A^2
140Surface tension:   0.105 kJ/mol/A
141Using charge/radii information from prmtop file
142
143 Number of triangulated 3-point waters found:        0
144
145--------------------------------------------------------------------------------
146   4.  RESULTS
147--------------------------------------------------------------------------------
148
149
150
151   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
152      1      -5.8138E+00     1.2397E+01     4.9493E+01     HB1        16
153
154 BOND    =        2.7553  ANGLE   =        0.0734  DIHED      =        0.4000
155 VDWAALS =       -0.2408  EEL     =        6.4144  EPB        =       -6.3802
156 1-4 VDW =        1.0466  1-4 EEL =      -17.0265  RESTRAINT  =        0.0000
157 ENPOLAR =        7.1439
158
159
160  Maximum number of minimization cycles reached.
161
162
163                    FINAL RESULTS
164
165
166
167   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
168      1      -5.8138E+00     1.2397E+01     4.9493E+01     HB1        16
169
170 BOND    =        2.7553  ANGLE   =        0.0734  DIHED      =        0.4000
171 VDWAALS =       -0.2408  EEL     =        6.4144  EPB        =       -6.3802
172 1-4 VDW =        1.0466  1-4 EEL =      -17.0265  RESTRAINT  =        0.0000
173 ENPOLAR =        7.1439
174
175--------------------------------------------------------------------------------
176   5.  TIMINGS
177--------------------------------------------------------------------------------
178
179|    Read coords time           0.00 ( 0.07% of Total)
180|             PB Nonbond                 0.78 (100.0% of Nonbo)
181|          Nonbond force              0.78 (100.0% of Force)
182|          Bond/Angle/Dihedral        0.00 ( 0.01% of Force)
183|       Force time                 0.78 (100.0% of Runmd)
184|    Runmd Time                 0.78 (99.65% of Total)
185|    Other                      0.00 ( 0.28% of Total)
186| Total time                 0.78 (100.0% of ALL  )
187
188| Highest rstack allocated:          0
189| Highest istack allocated:          0
190|           Job began  at 14:02:46.158  on 05/28/2008
191|           Setup done at 14:02:46.160  on 05/28/2008
192|           Run   done at 14:02:46.937  on 05/28/2008
193|     wallclock() was called      22 times
194