Hello,
I am using AmberTools17 on linux Mint 18, I am trying to run MD
simulations on the pdb file 3ibk, and i can't since I have a problem
with creation of topology and parameters files. Always some kind of
errors connected to "weird bonds" occur. The last one looks like this:
antechamber -i 3ibk.pdb -fi pdb -o 3ibk.mol2 -fo mol2 -c bcc -s 2
Welcome to antechamber 17.3: molecular input file processor.
acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for pdb File --
Status: pass
Warning: Detected more than 10 Residue sequence numbers;
this may be a large multiple residue PDB file;
large multiple residue PDB files are not supported.
Continuing, but problems may be encountered.
-- Check Unusual Elements --
Warning: Unusual element (K) for atom (ID: 521, Name: K).
Warning: Unusual element (K) for atom (ID: 522, Name: K).
GAFF does not have sufficient parameters for molecules having unusual
elements (those other than H,C,N,O,S,P and halogens).
To ensure antechamber works properly, one may need to designate
bond types for bonds involved with unusual elements.
To do so, simply freeze the bond types by appending "F" or "f"
to the corresponding bond types in ac or mol2 files.
-- Check Open Valences --
Status: pass
-- Check Geometry --
for those bonded
Warning: Large distance for BOND 21 O6 K 0 2.84 [1.42 - 2.31]
Warning: Large distance for BOND 22 O6 K 0 2.83 [1.42 - 2.31]
Warning: Large distance for BOND 23 O6 K 0 2.96 [1.42 - 2.31]
Warning: Large distance for BOND 24 O6 K 0 2.66 [1.42 - 2.31]
Warning: Large distance for BOND 25 O6 K 0 2.74 [1.42 - 2.31]
Warning: Large distance for BOND 26 O6 K 0 2.86 [1.42 - 2.31]
Warning: Large distance for BOND 27 O6 K 0 2.91 [1.42 - 2.31]
Warning: Large distance for BOND 28 O6 K 0 2.71 [1.42 - 2.31]
Warning: Large distance for BOND 49 O6 K 0 2.65 [1.42 - 2.31]
Warning: Large distance for BOND 50 O6 K 0 2.72 [1.42 - 2.31]
Warning: Large distance for BOND 51 O6 K 0 3.00 [1.42 - 2.31]
Warning: Large distance for BOND 52 O6 K 0 2.64 [1.42 - 2.31]
Warning: Large distance for BOND 53 O6 K 0 2.69 [1.42 - 2.31]
Warning: Large distance for BOND 54 O6 K 0 2.71 [1.42 - 2.31]
Warning: Large distance for BOND 55 O6 K 0 3.12 [1.42 - 2.31]
Warning: Large distance for BOND 56 O6 K 0 2.69 [1.42 - 2.31]
for those not bonded
Warning: Close ( 1.47) nonbonded atoms (ID: 19, Name: P) and (ID: 20,
Name: OP1).
Warning: Close ( 1.47) nonbonded atoms (ID: 19, Name: P) and (ID: 21,
Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 19, Name: P) and (ID: 22,
Name: O5').
Warning: Close ( 1.37) nonbonded atoms (ID: 22, Name: O5') and (ID:
23, Name: C5').
Warning: Close ( 1.51) nonbonded atoms (ID: 23, Name: C5') and (ID:
24, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 24, Name: C4') and (ID:
25, Name: O4').
Warning: Close ( 1.52) nonbonded atoms (ID: 24, Name: C4') and (ID:
26, Name: C3').
Warning: Close ( 1.42) nonbonded atoms (ID: 25, Name: O4') and (ID:
30, Name: C1').
Warning: Close ( 1.43) nonbonded atoms (ID: 26, Name: C3') and (ID:
27, Name: O3').
Warning: Close ( 1.51) nonbonded atoms (ID: 26, Name: C3') and (ID:
28, Name: C2').
Warning: Close ( 1.61) nonbonded atoms (ID: 27, Name: O3') and (ID:
41, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 28, Name: C2') and (ID:
29, Name: O2').
Warning: Close ( 1.52) nonbonded atoms (ID: 28, Name: C2') and (ID:
30, Name: C1').
Warning: Close ( 1.48) nonbonded atoms (ID: 30, Name: C1') and (ID:
31, Name: N9).
Warning: Close ( 1.38) nonbonded atoms (ID: 31, Name: N9) and (ID: 32,
Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 31, Name: N9) and (ID: 40,
Name: C4).
Warning: Close ( 1.32) nonbonded atoms (ID: 32, Name: C8) and (ID: 33,
Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 33, Name: N7) and (ID: 34,
Name: C5).
Warning: Close ( 1.40) nonbonded atoms (ID: 34, Name: C5) and (ID: 35,
Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 34, Name: C5) and (ID: 40,
Name: C4).
Warning: Close ( 1.32) nonbonded atoms (ID: 35, Name: C6) and (ID: 36,
Name: N6).
Warning: Close ( 1.33) nonbonded atoms (ID: 35, Name: C6) and (ID: 37,
Name: N1).
Warning: Close ( 1.33) nonbonded atoms (ID: 37, Name: N1) and (ID: 38,
Name: C2).
Warning: Close ( 1.33) nonbonded atoms (ID: 38, Name: C2) and (ID: 39,
Name: N3).
Warning: Close ( 1.34) nonbonded atoms (ID: 39, Name: N3) and (ID: 40,
Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 41, Name: P) and (ID: 42,
Name: OP1).
Warning: Close ( 1.49) nonbonded atoms (ID: 41, Name: P) and (ID: 43,
Name: OP2).
Warning: Close ( 1.59) nonbonded atoms (ID: 41, Name: P) and (ID: 44,
Name: O5').
Warning: Close ( 1.41) nonbonded atoms (ID: 44, Name: O5') and (ID:
45, Name: C5').
Warning: Close ( 1.51) nonbonded atoms (ID: 45, Name: C5') and (ID:
46, Name: C4').
Warning: Close ( 1.47) nonbonded atoms (ID: 46, Name: C4') and (ID:
47, Name: O4').
Warning: Close ( 1.55) nonbonded atoms (ID: 46, Name: C4') and (ID:
48, Name: C3').
Warning: Close ( 1.40) nonbonded atoms (ID: 47, Name: O4') and (ID:
52, Name: C1').
Warning: Close ( 1.45) nonbonded atoms (ID: 48, Name: C3') and (ID:
49, Name: O3').
Warning: Close ( 1.50) nonbonded atoms (ID: 48, Name: C3') and (ID:
50, Name: C2').
Warning: Close ( 1.62) nonbonded atoms (ID: 49, Name: O3') and (ID:
64, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 50, Name: C2') and (ID:
51, Name: O2').
Warning: Close ( 1.54) nonbonded atoms (ID: 50, Name: C2') and (ID:
52, Name: C1').
Warning: Close ( 1.47) nonbonded atoms (ID: 52, Name: C1') and (ID:
53, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 53, Name: N9) and (ID: 54,
Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 53, Name: N9) and (ID: 63,
Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 54, Name: C8) and (ID: 55,
Name: N7).
Warning: Close ( 1.38) nonbonded atoms (ID: 55, Name: N7) and (ID: 56,
Name: C5).
Warning: Close ( 1.41) nonbonded atoms (ID: 56, Name: C5) and (ID: 57,
Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 56, Name: C5) and (ID: 63,
Name: C4).
Warning: Close ( 1.24) nonbonded atoms (ID: 57, Name: C6) and (ID: 58,
Name: O6).
Warning: Close ( 1.40) nonbonded atoms (ID: 57, Name: C6) and (ID: 59,
Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 59, Name: N1) and (ID: 60,
Name: C2).
Warning: Close ( 1.34) nonbonded atoms (ID: 60, Name: C2) and (ID: 61,
Name: N2).
Warning: Close ( 1.32) nonbonded atoms (ID: 60, Name: C2) and (ID: 62,
Name: N3).
Warning: Close ( 1.37) nonbonded atoms (ID: 62, Name: N3) and (ID: 63,
Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 64, Name: P) and (ID: 65,
Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 64, Name: P) and (ID: 66,
Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 64, Name: P) and (ID: 67,
Name: O5').
Warning: Close ( 1.39) nonbonded atoms (ID: 67, Name: O5') and (ID:
68, Name: C5').
Warning: Close ( 1.51) nonbonded atoms (ID: 68, Name: C5') and (ID:
69, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 69, Name: C4') and (ID:
70, Name: O4').
Warning: Close ( 1.52) nonbonded atoms (ID: 69, Name: C4') and (ID:
71, Name: C3').
Warning: Close ( 1.42) nonbonded atoms (ID: 70, Name: O4') and (ID:
75, Name: C1').
Warning: Close ( 1.41) nonbonded atoms (ID: 71, Name: C3') and (ID:
72, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 71, Name: C3') and (ID:
73, Name: C2').
Warning: Close ( 1.59) nonbonded atoms (ID: 72, Name: O3') and (ID:
87, Name: P).
Warning: Close ( 1.43) nonbonded atoms (ID: 73, Name: C2') and (ID:
74, Name: O2').
Warning: Close ( 1.53) nonbonded atoms (ID: 73, Name: C2') and (ID:
75, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 75, Name: C1') and (ID:
76, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 76, Name: N9) and (ID: 77,
Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 76, Name: N9) and (ID: 86,
Name: C4).
Warning: Close ( 1.32) nonbonded atoms (ID: 77, Name: C8) and (ID: 78,
Name: N7).
Warning: Close ( 1.39) nonbonded atoms (ID: 78, Name: N7) and (ID: 79,
Name: C5).
Warning: Close ( 1.41) nonbonded atoms (ID: 79, Name: C5) and (ID: 80,
Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 79, Name: C5) and (ID: 86,
Name: C4).
Warning: Close ( 1.24) nonbonded atoms (ID: 80, Name: C6) and (ID: 81,
Name: O6).
Warning: Close ( 1.39) nonbonded atoms (ID: 80, Name: C6) and (ID: 82,
Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 82, Name: N1) and (ID: 83,
Name: C2).
Warning: Close ( 1.34) nonbonded atoms (ID: 83, Name: C2) and (ID: 84,
Name: N2).
Warning: Close ( 1.32) nonbonded atoms (ID: 83, Name: C2) and (ID: 85,
Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 85, Name: N3) and (ID: 86,
Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 87, Name: P) and (ID: 88,
Name: OP1).
Warning: Close ( 1.47) nonbonded atoms (ID: 87, Name: P) and (ID: 89,
Name: OP2).
Warning: Close ( 1.59) nonbonded atoms (ID: 87, Name: P) and (ID: 90,
Name: O5').
Warning: Close ( 1.42) nonbonded atoms (ID: 90, Name: O5') and (ID:
91, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 91, Name: C5') and (ID:
92, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 92, Name: C4') and (ID:
93, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 92, Name: C4') and (ID:
94, Name: C3').
Warning: Close ( 1.39) nonbonded atoms (ID: 93, Name: O4') and (ID:
98, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 94, Name: C3') and (ID:
95, Name: O3').
Warning: Close ( 1.50) nonbonded atoms (ID: 94, Name: C3') and (ID:
96, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 95, Name: O3') and (ID:
110, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 96, Name: C2') and (ID:
97, Name: O2').
Warning: Close ( 1.53) nonbonded atoms (ID: 96, Name: C2') and (ID:
98, Name: C1').
Warning: Close ( 1.47) nonbonded atoms (ID: 98, Name: C1') and (ID:
99, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 99, Name: N9) and (ID:
100, Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 99, Name: N9) and (ID:
109, Name: C4).
Warning: Close ( 1.29) nonbonded atoms (ID: 100, Name: C8) and (ID:
101, Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 101, Name: N7) and (ID:
102, Name: C5).
Warning: Close ( 1.42) nonbonded atoms (ID: 102, Name: C5) and (ID:
103, Name: C6).
Warning: Close ( 1.36) nonbonded atoms (ID: 102, Name: C5) and (ID:
109, Name: C4).
Warning: Close ( 1.24) nonbonded atoms (ID: 103, Name: C6) and (ID:
104, Name: O6).
Warning: Close ( 1.40) nonbonded atoms (ID: 103, Name: C6) and (ID:
105, Name: N1).
Warning: Close ( 1.37) nonbonded atoms (ID: 105, Name: N1) and (ID:
106, Name: C2).
Warning: Close ( 1.36) nonbonded atoms (ID: 106, Name: C2) and (ID:
107, Name: N2).
Warning: Close ( 1.34) nonbonded atoms (ID: 106, Name: C2) and (ID:
108, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 108, Name: N3) and (ID:
109, Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 110, Name: P) and (ID:
111, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 110, Name: P) and (ID:
112, Name: OP2).
Warning: Close ( 1.56) nonbonded atoms (ID: 110, Name: P) and (ID:
113, Name: O5').
Warning: Close ( 1.37) nonbonded atoms (ID: 113, Name: O5') and (ID:
114, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 114, Name: C5') and (ID:
115, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 115, Name: C4') and (ID:
116, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 115, Name: C4') and (ID:
117, Name: C3').
Warning: Close ( 1.39) nonbonded atoms (ID: 116, Name: O4') and (ID:
121, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 117, Name: C3') and (ID:
118, Name: O3').
Warning: Close ( 1.55) nonbonded atoms (ID: 117, Name: C3') and (ID:
119, Name: C2').
Warning: Close ( 1.61) nonbonded atoms (ID: 118, Name: O3') and (ID:
130, Name: P).
Warning: Close ( 1.40) nonbonded atoms (ID: 119, Name: C2') and (ID:
120, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 119, Name: C2') and (ID:
121, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 121, Name: C1') and (ID:
122, Name: N1).
Warning: Close ( 1.39) nonbonded atoms (ID: 122, Name: N1) and (ID:
123, Name: C2).
Warning: Close ( 1.38) nonbonded atoms (ID: 122, Name: N1) and (ID:
129, Name: C6).
Warning: Close ( 1.22) nonbonded atoms (ID: 123, Name: C2) and (ID:
124, Name: O2).
Warning: Close ( 1.36) nonbonded atoms (ID: 123, Name: C2) and (ID:
125, Name: N3).
Warning: Close ( 1.37) nonbonded atoms (ID: 125, Name: N3) and (ID:
126, Name: C4).
Warning: Close ( 1.20) nonbonded atoms (ID: 126, Name: C4) and (ID:
127, Name: O4).
Warning: Close ( 1.43) nonbonded atoms (ID: 126, Name: C4) and (ID:
128, Name: C5).
Warning: Close ( 1.32) nonbonded atoms (ID: 128, Name: C5) and (ID:
129, Name: C6).
Warning: Close ( 1.48) nonbonded atoms (ID: 130, Name: P) and (ID:
131, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 130, Name: P) and (ID:
132, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 130, Name: P) and (ID:
133, Name: O5').
Warning: Close ( 1.41) nonbonded atoms (ID: 133, Name: O5') and (ID:
134, Name: C5').
Warning: Close ( 1.52) nonbonded atoms (ID: 134, Name: C5') and (ID:
135, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 135, Name: C4') and (ID:
136, Name: O4').
Warning: Close ( 1.52) nonbonded atoms (ID: 135, Name: C4') and (ID:
137, Name: C3').
Warning: Close ( 1.43) nonbonded atoms (ID: 136, Name: O4') and (ID:
141, Name: C1').
Warning: Close ( 1.40) nonbonded atoms (ID: 137, Name: C3') and (ID:
138, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 137, Name: C3') and (ID:
139, Name: C2').
Warning: Close ( 1.61) nonbonded atoms (ID: 138, Name: O3') and (ID:
150, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 139, Name: C2') and (ID:
140, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 139, Name: C2') and (ID:
141, Name: C1').
Warning: Close ( 1.50) nonbonded atoms (ID: 141, Name: C1') and (ID:
142, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 142, Name: N1) and (ID:
143, Name: C2).
Warning: Close ( 1.38) nonbonded atoms (ID: 142, Name: N1) and (ID:
149, Name: C6).
Warning: Close ( 1.22) nonbonded atoms (ID: 143, Name: C2) and (ID:
144, Name: O2).
Warning: Close ( 1.37) nonbonded atoms (ID: 143, Name: C2) and (ID:
145, Name: N3).
Warning: Close ( 1.39) nonbonded atoms (ID: 145, Name: N3) and (ID:
146, Name: C4).
Warning: Close ( 1.23) nonbonded atoms (ID: 146, Name: C4) and (ID:
147, Name: O4).
Warning: Close ( 1.44) nonbonded atoms (ID: 146, Name: C4) and (ID:
148, Name: C5).
Warning: Close ( 1.34) nonbonded atoms (ID: 148, Name: C5) and (ID:
149, Name: C6).
Warning: Close ( 1.48) nonbonded atoms (ID: 150, Name: P) and (ID:
151, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 150, Name: P) and (ID:
152, Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 150, Name: P) and (ID:
153, Name: O5').
Warning: Close ( 1.40) nonbonded atoms (ID: 153, Name: O5') and (ID:
154, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 154, Name: C5') and (ID:
155, Name: C4').
Warning: Close ( 1.46) nonbonded atoms (ID: 155, Name: C4') and (ID:
156, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 155, Name: C4') and (ID:
157, Name: C3').
Warning: Close ( 1.39) nonbonded atoms (ID: 156, Name: O4') and (ID:
161, Name: C1').
Warning: Close ( 1.40) nonbonded atoms (ID: 157, Name: C3') and (ID:
158, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 157, Name: C3') and (ID:
159, Name: C2').
Warning: Close ( 1.57) nonbonded atoms (ID: 158, Name: O3') and (ID:
172, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 159, Name: C2') and (ID:
160, Name: O2').
Warning: Close ( 1.52) nonbonded atoms (ID: 159, Name: C2') and (ID:
161, Name: C1').
Warning: Close ( 1.45) nonbonded atoms (ID: 161, Name: C1') and (ID:
162, Name: N9).
Warning: Close ( 1.36) nonbonded atoms (ID: 162, Name: N9) and (ID:
163, Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 162, Name: N9) and (ID:
171, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 163, Name: C8) and (ID:
164, Name: N7).
Warning: Close ( 1.39) nonbonded atoms (ID: 164, Name: N7) and (ID:
165, Name: C5).
Warning: Close ( 1.42) nonbonded atoms (ID: 165, Name: C5) and (ID:
166, Name: C6).
Warning: Close ( 1.37) nonbonded atoms (ID: 165, Name: C5) and (ID:
171, Name: C4).
Warning: Close ( 1.33) nonbonded atoms (ID: 166, Name: C6) and (ID:
167, Name: N6).
Warning: Close ( 1.36) nonbonded atoms (ID: 166, Name: C6) and (ID:
168, Name: N1).
Warning: Close ( 1.33) nonbonded atoms (ID: 168, Name: N1) and (ID:
169, Name: C2).
Warning: Close ( 1.34) nonbonded atoms (ID: 169, Name: C2) and (ID:
170, Name: N3).
Warning: Close ( 1.35) nonbonded atoms (ID: 170, Name: N3) and (ID:
171, Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 172, Name: P) and (ID:
173, Name: OP1).
Warning: Close ( 1.47) nonbonded atoms (ID: 172, Name: P) and (ID:
174, Name: OP2).
Warning: Close ( 1.59) nonbonded atoms (ID: 172, Name: P) and (ID:
175, Name: O5').
Warning: Close ( 1.37) nonbonded atoms (ID: 175, Name: O5') and (ID:
176, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 176, Name: C5') and (ID:
177, Name: C4').
Warning: Close ( 1.45) nonbonded atoms (ID: 177, Name: C4') and (ID:
178, Name: O4').
Warning: Close ( 1.54) nonbonded atoms (ID: 177, Name: C4') and (ID:
179, Name: C3').
Warning: Close ( 1.39) nonbonded atoms (ID: 178, Name: O4') and (ID:
183, Name: C1').
Warning: Close ( 1.43) nonbonded atoms (ID: 179, Name: C3') and (ID:
180, Name: O3').
Warning: Close ( 1.49) nonbonded atoms (ID: 179, Name: C3') and (ID:
181, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 180, Name: O3') and (ID:
195, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 181, Name: C2') and (ID:
182, Name: O2').
Warning: Close ( 1.54) nonbonded atoms (ID: 181, Name: C2') and (ID:
183, Name: C1').
Warning: Close ( 1.45) nonbonded atoms (ID: 183, Name: C1') and (ID:
184, Name: N9).
Warning: Close ( 1.38) nonbonded atoms (ID: 184, Name: N9) and (ID:
185, Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 184, Name: N9) and (ID:
194, Name: C4).
Warning: Close ( 1.30) nonbonded atoms (ID: 185, Name: C8) and (ID:
186, Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 186, Name: N7) and (ID:
187, Name: C5).
Warning: Close ( 1.40) nonbonded atoms (ID: 187, Name: C5) and (ID:
188, Name: C6).
Warning: Close ( 1.37) nonbonded atoms (ID: 187, Name: C5) and (ID:
194, Name: C4).
Warning: Close ( 1.22) nonbonded atoms (ID: 188, Name: C6) and (ID:
189, Name: O6).
Warning: Close ( 1.39) nonbonded atoms (ID: 188, Name: C6) and (ID:
190, Name: N1).
Warning: Close ( 1.36) nonbonded atoms (ID: 190, Name: N1) and (ID:
191, Name: C2).
Warning: Close ( 1.35) nonbonded atoms (ID: 191, Name: C2) and (ID:
192, Name: N2).
Warning: Close ( 1.34) nonbonded atoms (ID: 191, Name: C2) and (ID:
193, Name: N3).
Warning: Close ( 1.35) nonbonded atoms (ID: 193, Name: N3) and (ID:
194, Name: C4).
Warning: Close ( 1.48) nonbonded atoms (ID: 195, Name: P) and (ID:
196, Name: OP1).
Warning: Close ( 1.47) nonbonded atoms (ID: 195, Name: P) and (ID:
197, Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 195, Name: P) and (ID:
198, Name: O5').
Warning: Close ( 1.38) nonbonded atoms (ID: 198, Name: O5') and (ID:
199, Name: C5').
Warning: Close ( 1.49) nonbonded atoms (ID: 199, Name: C5') and (ID:
200, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 200, Name: C4') and (ID:
201, Name: O4').
Warning: Close ( 1.51) nonbonded atoms (ID: 200, Name: C4') and (ID:
202, Name: C3').
Warning: Close ( 1.41) nonbonded atoms (ID: 201, Name: O4') and (ID:
206, Name: C1').
Warning: Close ( 1.44) nonbonded atoms (ID: 202, Name: C3') and (ID:
203, Name: O3').
Warning: Close ( 1.53) nonbonded atoms (ID: 202, Name: C3') and (ID:
204, Name: C2').
Warning: Close ( 1.62) nonbonded atoms (ID: 203, Name: O3') and (ID:
218, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 204, Name: C2') and (ID:
205, Name: O2').
Warning: Close ( 1.52) nonbonded atoms (ID: 204, Name: C2') and (ID:
206, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 206, Name: C1') and (ID:
207, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 207, Name: N9) and (ID:
208, Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 207, Name: N9) and (ID:
217, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 208, Name: C8) and (ID:
209, Name: N7).
Warning: Close ( 1.39) nonbonded atoms (ID: 209, Name: N7) and (ID:
210, Name: C5).
Warning: Close ( 1.42) nonbonded atoms (ID: 210, Name: C5) and (ID:
211, Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 210, Name: C5) and (ID:
217, Name: C4).
Warning: Close ( 1.24) nonbonded atoms (ID: 211, Name: C6) and (ID:
212, Name: O6).
Warning: Close ( 1.40) nonbonded atoms (ID: 211, Name: C6) and (ID:
213, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 213, Name: N1) and (ID:
214, Name: C2).
Warning: Close ( 1.35) nonbonded atoms (ID: 214, Name: C2) and (ID:
215, Name: N2).
Warning: Close ( 1.33) nonbonded atoms (ID: 214, Name: C2) and (ID:
216, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 216, Name: N3) and (ID:
217, Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 218, Name: P) and (ID:
219, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 218, Name: P) and (ID:
220, Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 218, Name: P) and (ID:
221, Name: O5').
Warning: Close ( 1.41) nonbonded atoms (ID: 221, Name: O5') and (ID:
222, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 222, Name: C5') and (ID:
223, Name: C4').
Warning: Close ( 1.45) nonbonded atoms (ID: 223, Name: C4') and (ID:
224, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 223, Name: C4') and (ID:
225, Name: C3').
Warning: Close ( 1.43) nonbonded atoms (ID: 224, Name: O4') and (ID:
229, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 225, Name: C3') and (ID:
226, Name: O3').
Warning: Close ( 1.53) nonbonded atoms (ID: 225, Name: C3') and (ID:
227, Name: C2').
Warning: Close ( 1.59) nonbonded atoms (ID: 226, Name: O3') and (ID:
241, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 227, Name: C2') and (ID:
228, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 227, Name: C2') and (ID:
229, Name: C1').
Warning: Close ( 1.44) nonbonded atoms (ID: 229, Name: C1') and (ID:
230, Name: N9).
Warning: Close ( 1.38) nonbonded atoms (ID: 230, Name: N9) and (ID:
231, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 230, Name: N9) and (ID:
240, Name: C4).
Warning: Close ( 1.29) nonbonded atoms (ID: 231, Name: C8) and (ID:
232, Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 232, Name: N7) and (ID:
233, Name: C5).
Warning: Close ( 1.41) nonbonded atoms (ID: 233, Name: C5) and (ID:
234, Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 233, Name: C5) and (ID:
240, Name: C4).
Warning: Close ( 1.25) nonbonded atoms (ID: 234, Name: C6) and (ID:
235, Name: O6).
Warning: Close ( 1.39) nonbonded atoms (ID: 234, Name: C6) and (ID:
236, Name: N1).
Warning: Close ( 1.37) nonbonded atoms (ID: 236, Name: N1) and (ID:
237, Name: C2).
Warning: Close ( 1.34) nonbonded atoms (ID: 237, Name: C2) and (ID:
238, Name: N2).
Warning: Close ( 1.33) nonbonded atoms (ID: 237, Name: C2) and (ID:
239, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 239, Name: N3) and (ID:
240, Name: C4).
Warning: Close ( 1.49) nonbonded atoms (ID: 241, Name: P) and (ID:
242, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 241, Name: P) and (ID:
243, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 241, Name: P) and (ID:
244, Name: O5').
Warning: Close ( 1.53) nonbonded atoms (ID: 244, Name: O5') and (ID:
245, Name: C5').
Warning: Close ( 1.52) nonbonded atoms (ID: 245, Name: C5') and (ID:
246, Name: C4').
Warning: Close ( 1.45) nonbonded atoms (ID: 246, Name: C4') and (ID:
247, Name: O4').
Warning: Close ( 1.54) nonbonded atoms (ID: 246, Name: C4') and (ID:
248, Name: C3').
Warning: Close ( 1.40) nonbonded atoms (ID: 247, Name: O4') and (ID:
252, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 248, Name: C3') and (ID:
249, Name: O3').
Warning: Close ( 1.53) nonbonded atoms (ID: 248, Name: C3') and (ID:
250, Name: C2').
Warning: Close ( 1.41) nonbonded atoms (ID: 250, Name: C2') and (ID:
251, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 250, Name: C2') and (ID:
252, Name: C1').
Warning: Close ( 1.48) nonbonded atoms (ID: 252, Name: C1') and (ID:
253, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 253, Name: N1) and (ID:
254, Name: C2).
Warning: Close ( 1.38) nonbonded atoms (ID: 253, Name: N1) and (ID:
260, Name: C6).
Warning: Close ( 1.22) nonbonded atoms (ID: 254, Name: C2) and (ID:
255, Name: O2).
Warning: Close ( 1.37) nonbonded atoms (ID: 254, Name: C2) and (ID:
256, Name: N3).
Warning: Close ( 1.38) nonbonded atoms (ID: 256, Name: N3) and (ID:
257, Name: C4).
Warning: Close ( 1.23) nonbonded atoms (ID: 257, Name: C4) and (ID:
258, Name: O4).
Warning: Close ( 1.44) nonbonded atoms (ID: 257, Name: C4) and (ID:
259, Name: C5).
Warning: Close ( 1.34) nonbonded atoms (ID: 259, Name: C5) and (ID:
260, Name: C6).
Warning: Close ( 1.47) nonbonded atoms (ID: 279, Name: P) and (ID:
280, Name: OP1).
Warning: Close ( 1.46) nonbonded atoms (ID: 279, Name: P) and (ID:
281, Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 279, Name: P) and (ID:
282, Name: O5').
Warning: Close ( 1.42) nonbonded atoms (ID: 282, Name: O5') and (ID:
283, Name: C5').
Warning: Close ( 1.51) nonbonded atoms (ID: 283, Name: C5') and (ID:
284, Name: C4').
Warning: Close ( 1.43) nonbonded atoms (ID: 284, Name: C4') and (ID:
285, Name: O4').
Warning: Close ( 1.51) nonbonded atoms (ID: 284, Name: C4') and (ID:
286, Name: C3').
Warning: Close ( 1.43) nonbonded atoms (ID: 285, Name: O4') and (ID:
290, Name: C1').
Warning: Close ( 1.40) nonbonded atoms (ID: 286, Name: C3') and (ID:
287, Name: O3').
Warning: Close ( 1.51) nonbonded atoms (ID: 286, Name: C3') and (ID:
288, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 287, Name: O3') and (ID:
301, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 288, Name: C2') and (ID:
289, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 288, Name: C2') and (ID:
290, Name: C1').
Warning: Close ( 1.45) nonbonded atoms (ID: 290, Name: C1') and (ID:
291, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 291, Name: N9) and (ID:
292, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 291, Name: N9) and (ID:
300, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 292, Name: C8) and (ID:
293, Name: N7).
Warning: Close ( 1.39) nonbonded atoms (ID: 293, Name: N7) and (ID:
294, Name: C5).
Warning: Close ( 1.40) nonbonded atoms (ID: 294, Name: C5) and (ID:
295, Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 294, Name: C5) and (ID:
300, Name: C4).
Warning: Close ( 1.33) nonbonded atoms (ID: 295, Name: C6) and (ID:
296, Name: N6).
Warning: Close ( 1.34) nonbonded atoms (ID: 295, Name: C6) and (ID:
297, Name: N1).
Warning: Close ( 1.34) nonbonded atoms (ID: 297, Name: N1) and (ID:
298, Name: C2).
Warning: Close ( 1.32) nonbonded atoms (ID: 298, Name: C2) and (ID:
299, Name: N3).
Warning: Close ( 1.34) nonbonded atoms (ID: 299, Name: N3) and (ID:
300, Name: C4).
Warning: Close ( 1.46) nonbonded atoms (ID: 301, Name: P) and (ID:
302, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 301, Name: P) and (ID:
303, Name: OP2).
Warning: Close ( 1.57) nonbonded atoms (ID: 301, Name: P) and (ID:
304, Name: O5').
Warning: Close ( 1.38) nonbonded atoms (ID: 304, Name: O5') and (ID:
305, Name: C5').
Warning: Close ( 1.49) nonbonded atoms (ID: 305, Name: C5') and (ID:
306, Name: C4').
Warning: Close ( 1.42) nonbonded atoms (ID: 306, Name: C4') and (ID:
307, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 306, Name: C4') and (ID:
308, Name: C3').
Warning: Close ( 1.40) nonbonded atoms (ID: 307, Name: O4') and (ID:
312, Name: C1').
Warning: Close ( 1.40) nonbonded atoms (ID: 308, Name: C3') and (ID:
309, Name: O3').
Warning: Close ( 1.53) nonbonded atoms (ID: 308, Name: C3') and (ID:
310, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 309, Name: O3') and (ID:
324, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 310, Name: C2') and (ID:
311, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 310, Name: C2') and (ID:
312, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 312, Name: C1') and (ID:
313, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 313, Name: N9) and (ID:
314, Name: C8).
Warning: Close ( 1.36) nonbonded atoms (ID: 313, Name: N9) and (ID:
323, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 314, Name: C8) and (ID:
315, Name: N7).
Warning: Close ( 1.39) nonbonded atoms (ID: 315, Name: N7) and (ID:
316, Name: C5).
Warning: Close ( 1.40) nonbonded atoms (ID: 316, Name: C5) and (ID:
317, Name: C6).
Warning: Close ( 1.37) nonbonded atoms (ID: 316, Name: C5) and (ID:
323, Name: C4).
Warning: Close ( 1.23) nonbonded atoms (ID: 317, Name: C6) and (ID:
318, Name: O6).
Warning: Close ( 1.39) nonbonded atoms (ID: 317, Name: C6) and (ID:
319, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 319, Name: N1) and (ID:
320, Name: C2).
Warning: Close ( 1.35) nonbonded atoms (ID: 320, Name: C2) and (ID:
321, Name: N2).
Warning: Close ( 1.31) nonbonded atoms (ID: 320, Name: C2) and (ID:
322, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 322, Name: N3) and (ID:
323, Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 324, Name: P) and (ID:
325, Name: OP1).
Warning: Close ( 1.49) nonbonded atoms (ID: 324, Name: P) and (ID:
326, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 324, Name: P) and (ID:
327, Name: O5').
Warning: Close ( 1.39) nonbonded atoms (ID: 327, Name: O5') and (ID:
328, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 328, Name: C5') and (ID:
329, Name: C4').
Warning: Close ( 1.43) nonbonded atoms (ID: 329, Name: C4') and (ID:
330, Name: O4').
Warning: Close ( 1.49) nonbonded atoms (ID: 329, Name: C4') and (ID:
331, Name: C3').
Warning: Close ( 1.43) nonbonded atoms (ID: 330, Name: O4') and (ID:
335, Name: C1').
Warning: Close ( 1.39) nonbonded atoms (ID: 331, Name: C3') and (ID:
332, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 331, Name: C3') and (ID:
333, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 332, Name: O3') and (ID:
347, Name: P).
Warning: Close ( 1.40) nonbonded atoms (ID: 333, Name: C2') and (ID:
334, Name: O2').
Warning: Close ( 1.52) nonbonded atoms (ID: 333, Name: C2') and (ID:
335, Name: C1').
Warning: Close ( 1.47) nonbonded atoms (ID: 335, Name: C1') and (ID:
336, Name: N9).
Warning: Close ( 1.38) nonbonded atoms (ID: 336, Name: N9) and (ID:
337, Name: C8).
Warning: Close ( 1.38) nonbonded atoms (ID: 336, Name: N9) and (ID:
346, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 337, Name: C8) and (ID:
338, Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 338, Name: N7) and (ID:
339, Name: C5).
Warning: Close ( 1.42) nonbonded atoms (ID: 339, Name: C5) and (ID:
340, Name: C6).
Warning: Close ( 1.37) nonbonded atoms (ID: 339, Name: C5) and (ID:
346, Name: C4).
Warning: Close ( 1.22) nonbonded atoms (ID: 340, Name: C6) and (ID:
341, Name: O6).
Warning: Close ( 1.38) nonbonded atoms (ID: 340, Name: C6) and (ID:
342, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 342, Name: N1) and (ID:
343, Name: C2).
Warning: Close ( 1.35) nonbonded atoms (ID: 343, Name: C2) and (ID:
344, Name: N2).
Warning: Close ( 1.33) nonbonded atoms (ID: 343, Name: C2) and (ID:
345, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 345, Name: N3) and (ID:
346, Name: C4).
Warning: Close ( 1.48) nonbonded atoms (ID: 347, Name: P) and (ID:
348, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 347, Name: P) and (ID:
349, Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 347, Name: P) and (ID:
350, Name: O5').
Warning: Close ( 1.42) nonbonded atoms (ID: 350, Name: O5') and (ID:
351, Name: C5').
Warning: Close ( 1.51) nonbonded atoms (ID: 351, Name: C5') and (ID:
352, Name: C4').
Warning: Close ( 1.46) nonbonded atoms (ID: 352, Name: C4') and (ID:
353, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 352, Name: C4') and (ID:
354, Name: C3').
Warning: Close ( 1.41) nonbonded atoms (ID: 353, Name: O4') and (ID:
358, Name: C1').
Warning: Close ( 1.41) nonbonded atoms (ID: 354, Name: C3') and (ID:
355, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 354, Name: C3') and (ID:
356, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 355, Name: O3') and (ID:
370, Name: P).
Warning: Close ( 1.42) nonbonded atoms (ID: 356, Name: C2') and (ID:
357, Name: O2').
Warning: Close ( 1.53) nonbonded atoms (ID: 356, Name: C2') and (ID:
358, Name: C1').
Warning: Close ( 1.45) nonbonded atoms (ID: 358, Name: C1') and (ID:
359, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 359, Name: N9) and (ID:
360, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 359, Name: N9) and (ID:
369, Name: C4).
Warning: Close ( 1.30) nonbonded atoms (ID: 360, Name: C8) and (ID:
361, Name: N7).
Warning: Close ( 1.38) nonbonded atoms (ID: 361, Name: N7) and (ID:
362, Name: C5).
Warning: Close ( 1.40) nonbonded atoms (ID: 362, Name: C5) and (ID:
363, Name: C6).
Warning: Close ( 1.37) nonbonded atoms (ID: 362, Name: C5) and (ID:
369, Name: C4).
Warning: Close ( 1.24) nonbonded atoms (ID: 363, Name: C6) and (ID:
364, Name: O6).
Warning: Close ( 1.39) nonbonded atoms (ID: 363, Name: C6) and (ID:
365, Name: N1).
Warning: Close ( 1.37) nonbonded atoms (ID: 365, Name: N1) and (ID:
366, Name: C2).
Warning: Close ( 1.35) nonbonded atoms (ID: 366, Name: C2) and (ID:
367, Name: N2).
Warning: Close ( 1.32) nonbonded atoms (ID: 366, Name: C2) and (ID:
368, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 368, Name: N3) and (ID:
369, Name: C4).
Warning: Close ( 1.48) nonbonded atoms (ID: 370, Name: P) and (ID:
371, Name: OP1).
Warning: Close ( 1.47) nonbonded atoms (ID: 370, Name: P) and (ID:
372, Name: OP2).
Warning: Close ( 1.64) nonbonded atoms (ID: 370, Name: P) and (ID:
373, Name: O5').
Warning: Close ( 1.43) nonbonded atoms (ID: 373, Name: O5') and (ID:
374, Name: C5').
Warning: Close ( 1.52) nonbonded atoms (ID: 374, Name: C5') and (ID:
375, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 375, Name: C4') and (ID:
376, Name: O4').
Warning: Close ( 1.53) nonbonded atoms (ID: 375, Name: C4') and (ID:
377, Name: C3').
Warning: Close ( 1.40) nonbonded atoms (ID: 376, Name: O4') and (ID:
381, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 377, Name: C3') and (ID:
378, Name: O3').
Warning: Close ( 1.54) nonbonded atoms (ID: 377, Name: C3') and (ID:
379, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 378, Name: O3') and (ID:
390, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 379, Name: C2') and (ID:
380, Name: O2').
Warning: Close ( 1.52) nonbonded atoms (ID: 379, Name: C2') and (ID:
381, Name: C1').
Warning: Close ( 1.49) nonbonded atoms (ID: 381, Name: C1') and (ID:
382, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 382, Name: N1) and (ID:
383, Name: C2).
Warning: Close ( 1.38) nonbonded atoms (ID: 382, Name: N1) and (ID:
389, Name: C6).
Warning: Close ( 1.22) nonbonded atoms (ID: 383, Name: C2) and (ID:
384, Name: O2).
Warning: Close ( 1.37) nonbonded atoms (ID: 383, Name: C2) and (ID:
385, Name: N3).
Warning: Close ( 1.38) nonbonded atoms (ID: 385, Name: N3) and (ID:
386, Name: C4).
Warning: Close ( 1.23) nonbonded atoms (ID: 386, Name: C4) and (ID:
387, Name: O4).
Warning: Close ( 1.44) nonbonded atoms (ID: 386, Name: C4) and (ID:
388, Name: C5).
Warning: Close ( 1.34) nonbonded atoms (ID: 388, Name: C5) and (ID:
389, Name: C6).
Warning: Close ( 1.48) nonbonded atoms (ID: 390, Name: P) and (ID:
391, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 390, Name: P) and (ID:
392, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 390, Name: P) and (ID:
393, Name: O5').
Warning: Close ( 1.42) nonbonded atoms (ID: 393, Name: O5') and (ID:
394, Name: C5').
Warning: Close ( 1.52) nonbonded atoms (ID: 394, Name: C5') and (ID:
395, Name: C4').
Warning: Close ( 1.45) nonbonded atoms (ID: 395, Name: C4') and (ID:
396, Name: O4').
Warning: Close ( 1.52) nonbonded atoms (ID: 395, Name: C4') and (ID:
397, Name: C3').
Warning: Close ( 1.42) nonbonded atoms (ID: 396, Name: O4') and (ID:
401, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 397, Name: C3') and (ID:
398, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 397, Name: C3') and (ID:
399, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 398, Name: O3') and (ID:
410, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 399, Name: C2') and (ID:
400, Name: O2').
Warning: Close ( 1.53) nonbonded atoms (ID: 399, Name: C2') and (ID:
401, Name: C1').
Warning: Close ( 1.49) nonbonded atoms (ID: 401, Name: C1') and (ID:
402, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 402, Name: N1) and (ID:
403, Name: C2).
Warning: Close ( 1.38) nonbonded atoms (ID: 402, Name: N1) and (ID:
409, Name: C6).
Warning: Close ( 1.22) nonbonded atoms (ID: 403, Name: C2) and (ID:
404, Name: O2).
Warning: Close ( 1.37) nonbonded atoms (ID: 403, Name: C2) and (ID:
405, Name: N3).
Warning: Close ( 1.38) nonbonded atoms (ID: 405, Name: N3) and (ID:
406, Name: C4).
Warning: Close ( 1.23) nonbonded atoms (ID: 406, Name: C4) and (ID:
407, Name: O4).
Warning: Close ( 1.44) nonbonded atoms (ID: 406, Name: C4) and (ID:
408, Name: C5).
Warning: Close ( 1.34) nonbonded atoms (ID: 408, Name: C5) and (ID:
409, Name: C6).
Warning: Close ( 1.48) nonbonded atoms (ID: 410, Name: P) and (ID:
411, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 410, Name: P) and (ID:
412, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 410, Name: P) and (ID:
413, Name: O5').
Warning: Close ( 1.43) nonbonded atoms (ID: 413, Name: O5') and (ID:
414, Name: C5').
Warning: Close ( 1.52) nonbonded atoms (ID: 414, Name: C5') and (ID:
415, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 415, Name: C4') and (ID:
416, Name: O4').
Warning: Close ( 1.54) nonbonded atoms (ID: 415, Name: C4') and (ID:
417, Name: C3').
Warning: Close ( 1.39) nonbonded atoms (ID: 416, Name: O4') and (ID:
421, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 417, Name: C3') and (ID:
418, Name: O3').
Warning: Close ( 1.54) nonbonded atoms (ID: 417, Name: C3') and (ID:
419, Name: C2').
Warning: Close ( 1.61) nonbonded atoms (ID: 418, Name: O3') and (ID:
432, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 419, Name: C2') and (ID:
420, Name: O2').
Warning: Close ( 1.52) nonbonded atoms (ID: 419, Name: C2') and (ID:
421, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 421, Name: C1') and (ID:
422, Name: N9).
Warning: Close ( 1.37) nonbonded atoms (ID: 422, Name: N9) and (ID:
423, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 422, Name: N9) and (ID:
431, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 423, Name: C8) and (ID:
424, Name: N7).
Warning: Close ( 1.39) nonbonded atoms (ID: 424, Name: N7) and (ID:
425, Name: C5).
Warning: Close ( 1.41) nonbonded atoms (ID: 425, Name: C5) and (ID:
426, Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 425, Name: C5) and (ID:
431, Name: C4).
Warning: Close ( 1.34) nonbonded atoms (ID: 426, Name: C6) and (ID:
427, Name: N6).
Warning: Close ( 1.35) nonbonded atoms (ID: 426, Name: C6) and (ID:
428, Name: N1).
Warning: Close ( 1.34) nonbonded atoms (ID: 428, Name: N1) and (ID:
429, Name: C2).
Warning: Close ( 1.33) nonbonded atoms (ID: 429, Name: C2) and (ID:
430, Name: N3).
Warning: Close ( 1.34) nonbonded atoms (ID: 430, Name: N3) and (ID:
431, Name: C4).
Warning: Close ( 1.48) nonbonded atoms (ID: 432, Name: P) and (ID:
433, Name: OP1).
Warning: Close ( 1.49) nonbonded atoms (ID: 432, Name: P) and (ID:
434, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 432, Name: P) and (ID:
435, Name: O5').
Warning: Close ( 1.42) nonbonded atoms (ID: 435, Name: O5') and (ID:
436, Name: C5').
Warning: Close ( 1.51) nonbonded atoms (ID: 436, Name: C5') and (ID:
437, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 437, Name: C4') and (ID:
438, Name: O4').
Warning: Close ( 1.52) nonbonded atoms (ID: 437, Name: C4') and (ID:
439, Name: C3').
Warning: Close ( 1.41) nonbonded atoms (ID: 438, Name: O4') and (ID:
443, Name: C1').
Warning: Close ( 1.43) nonbonded atoms (ID: 439, Name: C3') and (ID:
440, Name: O3').
Warning: Close ( 1.51) nonbonded atoms (ID: 439, Name: C3') and (ID:
441, Name: C2').
Warning: Close ( 1.62) nonbonded atoms (ID: 440, Name: O3') and (ID:
455, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 441, Name: C2') and (ID:
442, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 441, Name: C2') and (ID:
443, Name: C1').
Warning: Close ( 1.48) nonbonded atoms (ID: 443, Name: C1') and (ID:
444, Name: N9).
Warning: Close ( 1.39) nonbonded atoms (ID: 444, Name: N9) and (ID:
445, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 444, Name: N9) and (ID:
454, Name: C4).
Warning: Close ( 1.32) nonbonded atoms (ID: 445, Name: C8) and (ID:
446, Name: N7).
Warning: Close ( 1.41) nonbonded atoms (ID: 446, Name: N7) and (ID:
447, Name: C5).
Warning: Close ( 1.43) nonbonded atoms (ID: 447, Name: C5) and (ID:
448, Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 447, Name: C5) and (ID:
454, Name: C4).
Warning: Close ( 1.25) nonbonded atoms (ID: 448, Name: C6) and (ID:
449, Name: O6).
Warning: Close ( 1.39) nonbonded atoms (ID: 448, Name: C6) and (ID:
450, Name: N1).
Warning: Close ( 1.39) nonbonded atoms (ID: 450, Name: N1) and (ID:
451, Name: C2).
Warning: Close ( 1.35) nonbonded atoms (ID: 451, Name: C2) and (ID:
452, Name: N2).
Warning: Close ( 1.31) nonbonded atoms (ID: 451, Name: C2) and (ID:
453, Name: N3).
Warning: Close ( 1.35) nonbonded atoms (ID: 453, Name: N3) and (ID:
454, Name: C4).
Warning: Close ( 1.48) nonbonded atoms (ID: 455, Name: P) and (ID:
456, Name: OP1).
Warning: Close ( 1.50) nonbonded atoms (ID: 455, Name: P) and (ID:
457, Name: OP2).
Warning: Close ( 1.58) nonbonded atoms (ID: 455, Name: P) and (ID:
458, Name: O5').
Warning: Close ( 1.40) nonbonded atoms (ID: 458, Name: O5') and (ID:
459, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 459, Name: C5') and (ID:
460, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 460, Name: C4') and (ID:
461, Name: O4').
Warning: Close ( 1.51) nonbonded atoms (ID: 460, Name: C4') and (ID:
462, Name: C3').
Warning: Close ( 1.42) nonbonded atoms (ID: 461, Name: O4') and (ID:
466, Name: C1').
Warning: Close ( 1.39) nonbonded atoms (ID: 462, Name: C3') and (ID:
463, Name: O3').
Warning: Close ( 1.50) nonbonded atoms (ID: 462, Name: C3') and (ID:
464, Name: C2').
Warning: Close ( 1.59) nonbonded atoms (ID: 463, Name: O3') and (ID:
478, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 464, Name: C2') and (ID:
465, Name: O2').
Warning: Close ( 1.51) nonbonded atoms (ID: 464, Name: C2') and (ID:
466, Name: C1').
Warning: Close ( 1.46) nonbonded atoms (ID: 466, Name: C1') and (ID:
467, Name: N9).
Warning: Close ( 1.38) nonbonded atoms (ID: 467, Name: N9) and (ID:
468, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 467, Name: N9) and (ID:
477, Name: C4).
Warning: Close ( 1.30) nonbonded atoms (ID: 468, Name: C8) and (ID:
469, Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 469, Name: N7) and (ID:
470, Name: C5).
Warning: Close ( 1.43) nonbonded atoms (ID: 470, Name: C5) and (ID:
471, Name: C6).
Warning: Close ( 1.37) nonbonded atoms (ID: 470, Name: C5) and (ID:
477, Name: C4).
Warning: Close ( 1.25) nonbonded atoms (ID: 471, Name: C6) and (ID:
472, Name: O6).
Warning: Close ( 1.40) nonbonded atoms (ID: 471, Name: C6) and (ID:
473, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 473, Name: N1) and (ID:
474, Name: C2).
Warning: Close ( 1.34) nonbonded atoms (ID: 474, Name: C2) and (ID:
475, Name: N2).
Warning: Close ( 1.33) nonbonded atoms (ID: 474, Name: C2) and (ID:
476, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 476, Name: N3) and (ID:
477, Name: C4).
Warning: Close ( 1.47) nonbonded atoms (ID: 478, Name: P) and (ID:
479, Name: OP1).
Warning: Close ( 1.48) nonbonded atoms (ID: 478, Name: P) and (ID:
480, Name: OP2).
Warning: Close ( 1.57) nonbonded atoms (ID: 478, Name: P) and (ID:
481, Name: O5').
Warning: Close ( 1.40) nonbonded atoms (ID: 481, Name: O5') and (ID:
482, Name: C5').
Warning: Close ( 1.50) nonbonded atoms (ID: 482, Name: C5') and (ID:
483, Name: C4').
Warning: Close ( 1.44) nonbonded atoms (ID: 483, Name: C4') and (ID:
484, Name: O4').
Warning: Close ( 1.52) nonbonded atoms (ID: 483, Name: C4') and (ID:
485, Name: C3').
Warning: Close ( 1.42) nonbonded atoms (ID: 484, Name: O4') and (ID:
489, Name: C1').
Warning: Close ( 1.42) nonbonded atoms (ID: 485, Name: C3') and (ID:
486, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 485, Name: C3') and (ID:
487, Name: C2').
Warning: Close ( 1.60) nonbonded atoms (ID: 486, Name: O3') and (ID:
501, Name: P).
Warning: Close ( 1.41) nonbonded atoms (ID: 487, Name: C2') and (ID:
488, Name: O2').
Warning: Close ( 1.53) nonbonded atoms (ID: 487, Name: C2') and (ID:
489, Name: C1').
Warning: Close ( 1.45) nonbonded atoms (ID: 489, Name: C1') and (ID:
490, Name: N9).
Warning: Close ( 1.39) nonbonded atoms (ID: 490, Name: N9) and (ID:
491, Name: C8).
Warning: Close ( 1.37) nonbonded atoms (ID: 490, Name: N9) and (ID:
500, Name: C4).
Warning: Close ( 1.31) nonbonded atoms (ID: 491, Name: C8) and (ID:
492, Name: N7).
Warning: Close ( 1.40) nonbonded atoms (ID: 492, Name: N7) and (ID:
493, Name: C5).
Warning: Close ( 1.41) nonbonded atoms (ID: 493, Name: C5) and (ID:
494, Name: C6).
Warning: Close ( 1.38) nonbonded atoms (ID: 493, Name: C5) and (ID:
500, Name: C4).
Warning: Close ( 1.24) nonbonded atoms (ID: 494, Name: C6) and (ID:
495, Name: O6).
Warning: Close ( 1.41) nonbonded atoms (ID: 494, Name: C6) and (ID:
496, Name: N1).
Warning: Close ( 1.39) nonbonded atoms (ID: 496, Name: N1) and (ID:
497, Name: C2).
Warning: Close ( 1.36) nonbonded atoms (ID: 497, Name: C2) and (ID:
498, Name: N2).
Warning: Close ( 1.32) nonbonded atoms (ID: 497, Name: C2) and (ID:
499, Name: N3).
Warning: Close ( 1.36) nonbonded atoms (ID: 499, Name: N3) and (ID:
500, Name: C4).
Warning: Close ( 1.48) nonbonded atoms (ID: 501, Name: P) and (ID:
502, Name: OP1).
Warning: Close ( 1.47) nonbonded atoms (ID: 501, Name: P) and (ID:
503, Name: OP2).
Warning: Close ( 1.60) nonbonded atoms (ID: 501, Name: P) and (ID:
504, Name: O5').
Warning: Close ( 1.42) nonbonded atoms (ID: 504, Name: O5') and (ID:
505, Name: C5').
Warning: Close ( 1.53) nonbonded atoms (ID: 505, Name: C5') and (ID:
506, Name: C4').
Warning: Close ( 1.47) nonbonded atoms (ID: 506, Name: C4') and (ID:
507, Name: O4').
Warning: Close ( 1.54) nonbonded atoms (ID: 506, Name: C4') and (ID:
508, Name: C3').
Warning: Close ( 1.42) nonbonded atoms (ID: 507, Name: O4') and (ID:
512, Name: C1').
Warning: Close ( 1.41) nonbonded atoms (ID: 508, Name: C3') and (ID:
509, Name: O3').
Warning: Close ( 1.52) nonbonded atoms (ID: 508, Name: C3') and (ID:
510, Name: C2').
Warning: Close ( 1.42) nonbonded atoms (ID: 510, Name: C2') and (ID:
511, Name: O2').
Warning: Close ( 1.53) nonbonded atoms (ID: 510, Name: C2') and (ID:
512, Name: C1').
Warning: Close ( 1.50) nonbonded atoms (ID: 512, Name: C1') and (ID:
513, Name: N1).
Warning: Close ( 1.38) nonbonded atoms (ID: 513, Name: N1) and (ID:
514, Name: C2).
Warning: Close ( 1.39) nonbonded atoms (ID: 513, Name: N1) and (ID:
520, Name: C6).
Warning: Close ( 1.22) nonbonded atoms (ID: 514, Name: C2) and (ID:
515, Name: O2).
Warning: Close ( 1.39) nonbonded atoms (ID: 514, Name: C2) and (ID:
516, Name: N3).
Warning: Close ( 1.39) nonbonded atoms (ID: 516, Name: N3) and (ID:
517, Name: C4).
Warning: Close ( 1.22) nonbonded atoms (ID: 517, Name: C4) and (ID:
518, Name: O4).
Warning: Close ( 1.44) nonbonded atoms (ID: 517, Name: C4) and (ID:
519, Name: C5).
Warning: Close ( 1.34) nonbonded atoms (ID: 519, Name: C5) and (ID:
520, Name: C6).
-- Check Weird Bonds --
/home/Applications/amber16/bin/to_be_dispatched/antechamber: Fatal Error!
Number of bonded atoms (7) for atom (ID: 521, Name: K) exceeds 6.
antechamber cannot handle such kinds of molecules.
Can you give me some advice?
p.s. I am a beginner in the field, so please take it into account
while explaining something
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Received on Tue Nov 14 2017 - 07:30:03 PST
