File: apbs-smol-surf.in

package info (click to toggle)
apbs 1.0.0-2
  • links: PTS, VCS
  • area: main
  • in suites: lenny
  • size: 38,840 kB
  • ctags: 7,893
  • sloc: ansic: 44,537; xml: 21,399; sh: 20,613; fortran: 17,796; yacc: 2,922; python: 2,804; makefile: 567; lex: 294; sed: 205; java: 134; awk: 26
file content (156 lines) | stat: -rw-r--r-- 2,912 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
##########################################################################
### PROTEIN KINASE INHIBITOR BINDING ENERGY -- MOLECULAR SURFACE
### $Id: apbs-smol-surf.in 1258 2008-04-10 17:50:16Z sdg0919 $
###
### Please see APBS documentation (http://apbs.sourceforge.net/doc/) for
### syntax help.
##########################################################################

read 
    mol pqr bx6_7_lig_apbs.pqr
    mol pqr bx6_7_apo_apbs.pqr
    mol pqr bx6_7_bin_apbs.pqr
end

# LIGAND ENERGY (FOCUSING)
elec name lig-coarse
    mg-manual
    dime 97 97 97 
    nlev 4
    glen 70 70 70
    gcent mol 3
    mol 1
    lpbe
    bcfl sdh
    ion charge 1 conc 0.000 radius 2.0     
    ion charge -1 conc 0.000 radius 2.0      
    pdie 2.0
    sdie 78.00
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end
elec name lig-fine
    mg-manual
    dime 97 97 97
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 1
    mol 1
    lpbe
    bcfl focus
    ion charge 1 conc 0.000 radius 2.0     
    ion charge -1 conc 0.000 radius 2.0        
    pdie 2.0
    sdie 78.00
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end

# KINASE ENERGY (FOCUSING)
elec name pka-coarse
    mg-manual
    dime 97 97 97
    nlev 4
    glen 70 70 70
    gcent mol 3
    mol 2
    lpbe
    bcfl sdh
    ion charge 1 conc 0.000 radius 2.0     
    ion charge -1 conc 0.000 radius 2.0    
    pdie 2.0
    sdie 78.00
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end
elec name pka-fine
    mg-manual
    dime 97 97 97
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 1
    mol 2
    lpbe
    bcfl focus
    ion charge 1 conc 0.000 radius 2.0     
    ion charge -1 conc 0.000 radius 2.0    
    pdie 2.0
    sdie 78.00
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end

# COMPLEX ENERGY (FOCUSING)
elec name complex-coarse
    mg-manual
    dime 97 97 97
    nlev 4
    glen 70 70 70
    gcent mol 3
    mol 3
    lpbe
    bcfl sdh
    ion charge 1 conc 0.000 radius 2.0
    ion charge -1 conc 0.000 radius 2.0
    pdie 2.0
    sdie 78.00
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end
elec name complex-fine
    mg-manual
    dime 97 97 97
    nlev 4
    grid 0.25 0.25 0.25
    gcent mol 1
    mol 3
    lpbe
    bcfl focus
    ion charge 1 conc 0.000 radius 2.0     
    ion charge -1 conc 0.000 radius 2.0    
    pdie 2.0
    sdie 78.00
    chgm spl0
    srfm smol
    srad 1.4
    swin 0.3
    sdens 10.0
    temp 298.15
    calcenergy total
    calcforce no
end

# COMBINE INTO BINDING ENERGY
print energy complex-fine - lig-fine - pka-fine end

quit