Mercurial > repos > marpiech > norwich_docking_tools
comparison tools/rdock/data/sf/RbtIonicAtoms.prm @ 2:0faa03a92843 draft default tip
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author | dzesikah |
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date | Fri, 26 Aug 2016 10:19:49 -0400 |
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1:ad4bc82457e5 | 2:0faa03a92843 |
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1 RBT_PARAMETER_FILE_V1.00 | |
2 TITLE Receptor ionic atom definitions | |
3 VERSION $Id: //depot/dev/client3/rdock/2013.1/data/sf/RbtIonicAtoms.prm#2 $ | |
4 ################################################################################ | |
5 # | |
6 # Revision history: | |
7 # | |
8 # 21 Nov 2001 (DM) Added Heme Fe entries | |
9 # 19 Oct 2001 (DM) Extended list of metal ions | |
10 # 13 Jun 2000 (DM) Branched from RbtRNAScoringFunction.prm | |
11 # New format for ionic atoms (separate section for each residue) | |
12 # | |
13 ################################################################################ | |
14 # Formal charges for RNA atoms | |
15 # | |
16 # A/ADE | |
17 # | |
18 SECTION A | |
19 O1P -0.5 | |
20 O2P -0.5 | |
21 END_SECTION | |
22 | |
23 SECTION ADE | |
24 O1P -0.5 | |
25 O2P -0.5 | |
26 END_SECTION | |
27 # | |
28 # C/CYT | |
29 # | |
30 SECTION C | |
31 O1P -0.5 | |
32 O2P -0.5 | |
33 END_SECTION | |
34 | |
35 SECTION CYT | |
36 O1P -0.5 | |
37 O2P -0.5 | |
38 END_SECTION | |
39 # | |
40 # G/GUA | |
41 # | |
42 SECTION G | |
43 O1P -0.5 | |
44 O2P -0.5 | |
45 END_SECTION | |
46 | |
47 SECTION GUA | |
48 O1P -0.5 | |
49 O2P -0.5 | |
50 END_SECTION | |
51 # | |
52 # U/URA | |
53 # | |
54 SECTION U | |
55 O1P -0.5 | |
56 O2P -0.5 | |
57 END_SECTION | |
58 | |
59 SECTION URA | |
60 O1P -0.5 | |
61 O2P -0.5 | |
62 END_SECTION | |
63 | |
64 ################################################################################# | |
65 # Formal charges for amino acids | |
66 # | |
67 # LYS+ | |
68 # | |
69 SECTION LYS | |
70 HZ1 +0.333 | |
71 HZ2 +0.333 | |
72 HZ3 +0.333 | |
73 END_SECTION | |
74 # | |
75 # ARG+ | |
76 # | |
77 SECTION ARG | |
78 HE +0.167 | |
79 HH11 +0.167 | |
80 HH12 +0.167 | |
81 HH21 +0.167 | |
82 HH22 +0.167 | |
83 CZ +0.167 | |
84 END_SECTION | |
85 # | |
86 # HSP+ | |
87 # | |
88 SECTION HSP | |
89 HD1 +0.333 | |
90 HE2 +0.333 | |
91 CE1 +0.333 | |
92 END_SECTION | |
93 | |
94 SECTION HIS | |
95 MANDATORY HD1,HE2 | |
96 HD1 +0.333 | |
97 HE2 +0.333 | |
98 CE1 +0.333 | |
99 END_SECTION | |
100 # | |
101 # ASP- | |
102 # | |
103 SECTION ASP | |
104 FORBIDDEN HD1,HD2 | |
105 OD1 -0.5 | |
106 OD2 -0.5 | |
107 END_SECTION | |
108 # | |
109 # GLU- | |
110 # | |
111 SECTION GLU | |
112 FORBIDDEN HE1,HE2 | |
113 OE1 -0.5 | |
114 OE2 -0.5 | |
115 END_SECTION | |
116 | |
117 ################################################################################# | |
118 # Formal charges for metal cations | |
119 # | |
120 SECTION NA | |
121 NA +1.0 | |
122 END_SECTION | |
123 | |
124 SECTION MG | |
125 MG +1.0 | |
126 END_SECTION | |
127 | |
128 SECTION K | |
129 K +1.0 | |
130 END_SECTION | |
131 | |
132 SECTION CA | |
133 CA +1.0 | |
134 END_SECTION | |
135 | |
136 SECTION V | |
137 V +1.0 | |
138 END_SECTION | |
139 | |
140 SECTION MN | |
141 MN +1.0 | |
142 END_SECTION | |
143 | |
144 SECTION FE | |
145 FE +1.0 | |
146 END_SECTION | |
147 | |
148 # Specific entries for GOLD PDB test set | |
149 SECTION FS4 | |
150 FE1 +1.0 | |
151 FE2 +1.0 | |
152 FE3 +1.0 | |
153 FE4 +1.0 | |
154 END_SECTION | |
155 | |
156 SECTION HEM | |
157 FE +1.0 | |
158 END_SECTION | |
159 | |
160 SECTION NI | |
161 NI +1.0 | |
162 END_SECTION | |
163 | |
164 SECTION ZN | |
165 ZN +1.0 | |
166 END_SECTION | |
167 | |
168 # Specific entries for ASTEX MOL2 test set | |
169 SECTION HG | |
170 HG +1.0 | |
171 END_SECTION | |
172 | |
173 SECTION CD | |
174 CD +1.0 | |
175 END_SECTION | |
176 | |
177 SECTION FS | |
178 FE1 +1.0 | |
179 FE2 +1.0 | |
180 FE3 +1.0 | |
181 FE4 +1.0 | |
182 END_SECTION | |
183 | |
184 SECTION CO | |
185 CO +1.0 | |
186 END_SECTION | |
187 | |
188 #These metals occur in undefined residues | |
189 SECTION UNK | |
190 MG +1.0 | |
191 MN +1.0 | |
192 ZN +1.0 | |
193 FE1 +1.0 | |
194 FE2 +1.0 | |
195 FE3 +1.0 | |
196 FE4 +1.0 | |
197 END_SECTION |