Dear all amber users
I encountered a problem in leap. When I convert a mol2 file to pdb format in
sybyl it lost its double bonds. However I used mol2 format for generating
gaff atom types and then frcmod file from parmchk.
Then I read prep and frcmod file in leap and then when tried to read
molecule .pdb file leap was crashed and gave me a message that bondatom
problem see atom.c file. I can't use mol2 format in leap so far I know.
I don't understand what happened.Could you please help me in this regard.
I enclosed mol2file, prep file and frcmod file of the molecule.
with regards.
Shafinaz F. Chowdhury, PhD
Research Associate,
Computational Chemistry,
Biotechnology Research Institute,
National Research Council of Canada.
Email: shafinaz.bri.nrc.ca
Tel: 514 496 6338
Fax: 514 496 5174
I.<TRIPOS>MOLECULE
****
42 44 1 1 3
PROTEIN
DICT_CHARGES
INVALID_CHARGES
.<TRIPOS>DICT
PROTEIN Amber95Protein
.<TRIPOS>ATOM
1 C 25.5593 3.0383 51.3643 C.ar 1
-0.1308
2 C 24.7971 3.6760 50.3684 C.ar 1 INH
0.1992
3 C 23.3924 3.7980 50.5501 C.ar 1 INH
0.1498
4 C 22.7918 3.2672 51.7148 C.ar 1
-0.1021
5 C 23.5907 2.6645 52.7025 C.ar 1
-0.1308
6 C 24.9907 2.6168 52.5789 C.ar 1
-0.0131
7 O7 25.4855 4.0986 49.2599 O.3 1
-0.3306
8 O8 22.5804 4.3631 49.6245 O.3 1
-0.5958
9 C9 25.7848 1.7740 53.4799 C.2 1
-0.1984
10 C10 25.5896 0.4284 53.5443 C.2 1
-0.0876
11 C11 26.6209 -0.4440 54.1574 C.2 1 INH
0.9116
12 N12 27.1615 -1.3917 53.3926 N.3 1
-1.0269
13 O13 26.8857 -0.3571 55.3538 O.2 1
-0.6275
14 C14 21.2815 3.2672 51.8918 C.3 1
-0.0668
15 S15 20.5287 2.0799 50.7489 S.3 1
-0.1152
16 C16 18.7922 2.2695 51.0309 C.2 1 INH
0.1317
17 N17 17.9972 1.1900 51.3659 N.2 1
-0.2862
18 C18 16.7040 1.6206 51.4837 C.ar 1 INH
0.2868
19 C19 16.5307 2.9763 51.2459 C.ar 1 INH
0.0104
20 S20 17.9957 3.8518 50.8275 S.3 1
-0.0303
21 C21 15.6400 0.7947 51.8772 C.ar 1
-0.2357
22 C22 14.3669 1.3827 52.0230 C.ar 1
-0.1517
23 C23 14.1817 2.7612 51.7748 C.ar 1
-0.1517
24 C24 15.2665 3.5707 51.3791 C.ar 1
-0.2357
25 C25 24.9479 4.7087 48.1002 C.3 1
-0.0713
26 H27 24.2363 4.0347 47.6225 H 1 INH
0.0829
27 H28 25.7509 4.9240 47.3994 H 1 INH
0.0829
28 H29 24.4555 5.6443 48.3655 H 1 INH
0.0829
29 H30 21.6581 4.2857 49.8780 H 1 INH
0.4686
30 C31 24.3281 -0.2393 53.2806 C.1 1 INH
0.3516
31 N32 22.9951 -0.8603 52.9873 N.1 1
-0.4832
32 H33 26.8929 -1.4775 52.4231 H 1 INH
0.4035
33 H34 27.8227 -2.0376 53.7988 H 1 INH
0.4035
34 H1 26.6192 2.9127 51.2059 H 1 INH
0.1768
35 H2 23.1184 2.2152 53.5630 H 1 INH
0.1768
36 H3 26.7981 2.0900 53.6917 H 1 INH
0.2085
37 H4 20.9037 4.2714 51.6988 H 1 INH
0.1239
38 H5 21.0407 2.9862 52.9170 H 1 INH
0.1239
39 H6 15.7962 -0.2533 52.0867 H 1 INH
0.1974
40 H7 13.5280 0.7806 52.3407 H 1 INH
0.1508
41 H8 13.2022 3.2014 51.9009 H 1 INH
0.1508
42 H9 15.1306 4.6258 51.1948 H 1 INH
0.1974
.<TRIPOS>BOND
1 1 2 ar
2 1 6 ar
3 1 34 1
4 6 9 1
5 6 5 ar
6 5 35 1
7 5 4 ar
8 4 14 1
9 4 3 ar
10 3 8 1
11 3 2 ar
12 2 7 1
13 7 25 1
14 25 26 1
15 25 27 1
16 25 28 1
17 8 29 1
18 14 15 1
19 14 37 1
20 14 38 1
21 15 16 1
22 16 17 2
23 16 20 1
24 20 19 1
25 19 24 ar
26 19 18 ar
27 18 21 ar
28 18 17 1
29 21 39 1
30 21 22 ar
31 22 40 1
32 22 23 ar
33 23 41 1
34 23 24 ar
35 24 42 1
36 9 10 2
37 9 36 1
38 10 11 1
39 10 30 1
40 30 31 3
41 11 12 1
42 11 13 2
43 12 32 1
44 12 33 1
.<TRIPOS>SUBSTRUCTURE
1 INH 1 PERM 0 **** **** 0 ROOT
.<TRIPOS>SET
LAB$A_SUBNAME STATIC SUBSTS LABELGROUP SYSTEM
0
ALL_AT_SUBS STATIC SUBSTS <user> ****
267 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 1
HOT STATIC ATOMS <user> ****
950 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \
0 0 0 0 0 0 0 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
.<TRIPOS>NORMAL
.<TRIPOS>ALT_TYPE
AMBER95_ALL_ALT_TYPE_SET
AMBER95_ALL 1 CA 2 CA 3 CA 4 CA 5 CA 6 CA 7 OS 8 OH 9 CD 10 CL 11 C 12 N \
13 O 14 CT 15 S 16 CA 17 NB 18 CA 19 CA 20 SA 21 CA 22 CA \
23 CA 24 CA 25 CT 26 H1 27 H1 28 H1 29 HO 30 CY 31 NY \
32 H 33 H 34 HA 35 HA 36 HA 37 H1 38 H1 39 HA 40 HA 41 HA \
42 HA
FRCMODFILE===
remark goes here
MASS
BOND
n3-c 492.90 1.340 same as c2-n3
cd-c1 416.90 1.430 same as c1-c2
n1-c1 1006.5 1.14 same as n1-c1
ca-nb 467.4 1.352 same as ca-nb
ANGLE
n3-c -cd 67.125 114.880 Calculated with empirical approach
hn-n3-c 47.800 119.380 same as c2-n3-hn
c -cd-c1 64.635 117.825 Calculated with empirical approach
c -cd-cd 65.000 123.470 same as c2-cd-cd
cd-c1-n1 80.000 180.000 Calculated with empirical approach
cd-cd-ca 65.000 123.130 same as c2-cd-ca
c1-cd-cd 65.000 124.800 Calculated with empirical approach
ca-os-c3 62.700 118.150 same as c2-os-c3
ca-c3-h1 47.300 109.050 same as c2-c3-h1
ca-c3-ss 66.164 109.580 Calculated with empirical approach
ss-ca-nb 66.691 121.945 Calculated with empirical approach
DIHE
n3-c -cd-c1 1 1.000 180.000 2.000 same as
X -c2-cd-X
n3-c -cd-cd 1 1.000 180.000 2.000 same as
X -c2-cd-X
hn-n3-c -o 1 0.300 180.000 2.000 same as
X -c2-n3-X
hn-n3-c -cd 1 0.300 180.000 2.000 same as
X -c2-n3-X
c -cd-c1-n1 1 0.000 180.000 2.000 same as
X -c1-c2-X
o -c -cd-c1 1 1.000 180.000 2.000 same as
X -c2-cd-X
o -c -cd-cd 1 1.000 180.000 2.000 same as
X -c2-cd-X
cd-cd-ca-ca 1 2.550 180.000 2.000 same as
X -c2-ca-X
n1-c1-cd-cd 1 0.000 180.000 2.000 same as
X -c1-c2-X
ha-cd-ca-ca 1 2.550 180.000 2.000 same as
X -c2-ca-X
IMPROPER
c1-c -cd-cd 1.1 180.0 2.0 Using default
value
ca-cd-cd-ha 1.1 180.0 2.0 Using default
value
ca-ca-ca-cd 1.1 180.0 2.0 Using default
value
ca-ca-ca-ha 1.1 180.0 2.0 Using default
value
ca-ca-ca-os 1.1 180.0 2.0 Using default
value
ca-ca-ca-oh 1.1 180.0 2.0 Using default
value
nb-ss-ca-ss 1.1 180.0 2.0 Using default
value
ca-ca-ca-nb 1.1 180.0 2.0 Using default
value
ca-ca-ca-ss 1.1 180.0 2.0 Using default
value
NONBON
prep file =====================
0 0 2
This is a remark line
molecule.res
INH XYZ 0
CORRECT OMIT DU BEG
0.0000
1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
4 N12 n3 M 3 2 1 1.540 111.208 180.000 -1.027
5 H33 hn E 4 3 2 1.010 74.558 84.933 0.404
6 H34 hn E 4 3 2 1.009 130.903 -32.149 0.404
7 C11 c M 4 3 2 1.332 66.043 -141.134 0.912
8 O13 o E 7 4 3 1.229 121.419 123.223 -0.627
9 C10 cd M 7 4 3 1.483 117.624 -51.235 -0.088
10 C31 c1 S 9 7 4 1.451 114.153 70.674 0.352
11 N32 n1 E 10 9 7 1.500 177.044 175.093 -0.483
12 C9 cd M 9 7 4 1.362 120.077 -120.222 -0.198
13 H3 ha E 12 9 7 1.082 114.428 13.108 0.208
14 C ca M 12 9 7 1.467 121.288 163.115 -0.013
15 C ca S 14 12 9 1.406 120.251 59.441 -0.131
16 H2 ha E 15 14 12 1.079 119.514 10.421 0.177
17 C ca M 14 12 9 1.406 118.957 -101.035 -0.131
18 H1 ha E 17 14 12 1.079 119.263 -12.601 0.177
19 C ca M 17 14 12 1.407 121.925 170.404 0.199
20 O7 os S 19 17 14 1.371 116.115 176.705 -0.331
21 C25 c3 3 20 19 17 1.416 127.190 176.967 -0.071
22 H27 h1 E 21 20 19 1.090 109.856 -60.394 0.083
23 H28 h1 E 21 20 19 1.087 109.460 -179.812 0.083
24 H29 h1 E 21 20 19 1.089 109.980 60.826 0.083
25 C ca M 19 17 14 1.422 118.908 -5.318 0.150
26 O8 oh S 25 19 17 1.355 122.711 -178.051 -0.596
27 H30 ho E 26 25 19 0.959 111.192 174.696 0.469
28 C ca M 25 19 17 1.414 119.506 -0.619 -0.102
29 C14 c3 M 28 25 19 1.520 121.157 -174.567 -0.067
30 H4 h1 E 29 28 25 1.090 108.893 -50.758 0.124
31 H5 h1 E 29 28 25 1.090 109.216 -169.816 0.124
32 S15 ss M 29 28 25 1.812 109.837 70.178 -0.115
33 C16 ca M 32 29 28 1.770 103.734 -177.287 0.132
34 S20 ss E 33 32 29 1.783 120.976 57.588 -0.030
35 N17 nb M 33 32 29 1.381 121.333 -124.876 -0.286
36 C18 ca M 35 33 32 1.368 108.587 -178.260 0.287
37 C19 ca M 36 35 33 1.387 114.267 0.020 0.010
38 C24 ca M 37 36 35 1.403 120.693 -177.622 -0.236
39 H9 ha E 38 37 36 1.080 120.775 179.938 0.197
40 C23 ca M 38 37 36 1.411 118.418 0.717 -0.152
41 H8 ha E 40 38 37 1.082 119.735 178.928 0.151
42 C22 ca M 40 38 37 1.412 120.582 -0.362 -0.152
43 H7 ha E 42 40 38 1.080 119.577 179.015 0.151
44 C21 ca M 42 40 38 1.410 120.467 -0.069 -0.236
45 H6 ha E 44 42 40 1.080 120.993 178.539 0.197
LOOP
C C
C19 S20
C21 C18
IMPROPER
C10 N12 C11 O13
C31 C11 C10 C9
C C10 C9 H3
C C C C9
C C C H2
C C C H1
C C C O7
C C C O8
C14 C C C
N17 S15 C16 S20
C19 C21 C18 N17
C18 C24 C19 S20
C19 C23 C24 H9
C24 C22 C23 H8
C23 C21 C22 H7
C18 C22 C21 H6
DONE
STOP
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Received on Wed Sep 24 2003 - 20:53:01 PDT
