I am trying to load a complex into amber. I followed the directions as
posted previously.
>From reading the mailing archives this is supposed to be caused by the
names in the .mol2 file not matching those in the PDB.
I can't seem to see where there is a difference or why I am getting this
error... I used the same part of the PDB to create the mol2, from what I
can see I can't figure out what is wrong...
Here is the error:
FATAL: Atom .R<DIZ 112>.A<CL1 1> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C1 2> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C2 3> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C3 4> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C4 5> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C5 6> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C6 7> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C7 8> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C8 9> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O1 10> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O2 11> does not have a type.
FATAL: Atom .R<DIZ 112>.A<N1 12> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C9 13> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O3 14> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C10 15> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C11 16> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C12 17> does not have a type.
FATAL: Atom .R<DIZ 112>.A<I1 18> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C13 19> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C14 20> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C15 21> does not have a type.
FATAL: Atom .R<DIZ 112>.A<N2 22> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C16 23> does not have a type.
FATAL: Atom .R<DIZ 112>.A<O4 24> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C17 25> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C18 26> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C19 27> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C20 28> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C21 29> does not have a type.
FATAL: Atom .R<DIZ 112>.A<CL2 30> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C22 31> does not have a type.
FATAL: Atom .R<DIZ 112>.A<C23 32> does not have a type.
Here is the top of the mol2 file
.<TRIPOS>MOLECULE
DIZ
47 50 1 0 0
SMALL
bcc
.<TRIPOS>ATOM
1 CL1 46.9900 12.5070 23.9630 cl 112 DIZ -0.082400
2 C1 46.4590 13.0780 25.4790 ca 112 DIZ 0.030400
3 C2 45.4730 14.0890 25.5250 ca 112 DIZ -0.127000
4 C3 44.9950 14.5530 26.7710 ca 112 DIZ -0.103000
5 C4 45.5070 14.0040 28.0100 ca 112 DIZ -0.121300
6 C5 46.5220 12.9920 27.9340 ca 112 DIZ -0.103000
7 C6 46.9930 12.5320 26.6690 ca 112 DIZ -0.127000
8 C7 44.9600 14.4310 29.3870 c3 112 DIZ 0.111000
9 C8 44.4820 15.9000 29.4790 c 112 DIZ 0.622100
10 O1 45.1280 16.8830 29.1700 o 112 DIZ -0.524000
11 O2 43.2240 16.0420 29.9500 oh 112 DIZ -0.607100
12 N1 43.8710 13.3990 29.7940 n 112 DIZ -0.462800
13 C9 44.0370 12.7710 31.0370 c 112 DIZ 0.726100
14 O3 44.9980 13.0330 31.7820 o 112 DIZ -0.627500
15 C10 43.0860 11.7530 31.5240 ca 112 DIZ -0.168600
16 C11 43.6710 10.6720 32.2090 ca 112 DIZ -0.020000
17 C12 42.8840 9.6360 32.7030 ca 112 DIZ -0.013100
18 I1 43.8310 8.1200 33.6790 i 112 DIZ -0.120900
19 C13 41.4860 9.6330 32.5270 ca 112 DIZ -0.044000
20 C14 40.8780 10.7200 31.8340 ca 112 DIZ -0.187000
21 C15 41.6750 11.7920 31.3250 ca 112 DIZ 0.124600
22 N2 40.9860 12.8020 30.6500 n 112 DIZ -0.465100
23 C16 41.3750 13.4730 29.5120 c 112 DIZ 0.692500
24 O4 40.6240 14.3350 29.0510 o 112 DIZ -0.607500
25 C17 42.7390 13.1510 28.8060 c3 112 DIZ 0.099000
26 C18 42.7140 11.7920 28.0130 ca 112 DIZ -0.112300
27 C19 43.9110 11.0910 27.7240 ca 112 DIZ -0.110000
28 C20 43.9440 9.9000 26.9940 ca 112 DIZ -0.120500
29 C21 42.7660 9.3640 26.5180 ca 112 DIZ 0.024400
30 CL2 42.8510 7.9550 25.6170 cl 112 DIZ -0.084400
31 C22 41.5290 9.9890 26.7720 ca 112 DIZ -0.120500
32 C23 41.5020 11.2040 27.5210 ca 112 DIZ -0.110000
33 HO2 43.0710 16.9950 30.2110 ho 112 DIZ 0.454000
34 HN2 40.1050 13.0700 31.0400 hn 112 DIZ 0.329500
35 H7 45.7880 14.4200 30.1110 h1 112 DIZ 0.141700
36 H6 47.7700 11.7550 26.6190 ha 112 DIZ 0.153500
37 H5 46.9400 12.5680 28.8590 ha 112 DIZ 0.154500
38 H3 44.2260 15.3390 26.8010 ha 112 DIZ 0.154500
39 H23 40.5390 11.6960 27.7230 ha 112 DIZ 0.148000
40 H22 40.5950 9.5460 26.3970 ha 112 DIZ 0.152500
41 H20 44.9020 9.3940 26.8010 ha 112 DIZ 0.152500
42 H2 45.0780 14.5150 24.5910 ha 112 DIZ 0.153500
43 H19 44.8610 11.5050 28.0930 ha 112 DIZ 0.148000
44 H17 42.9370 13.8440 27.9750 h1 112 DIZ 0.130700
45 H14 39.7880 10.7340 31.6900 ha 112 DIZ 0.146000
46 H13 40.8750 8.8060 32.9180 ha 112 DIZ 0.153000
47 H11 44.7610 10.6460 32.3550 ha 112 DIZ 0.170000
and here is the portion from the PDB
HETATM 1571 CL1 DIZ 112 46.990 12.507 23.963 1.00 23.67
CL
HETATM 1572 C1 DIZ 112 46.459 13.078 25.479 1.00 19.71
C
HETATM 1573 C2 DIZ 112 45.473 14.089 25.525 1.00 20.30
C
HETATM 1574 C3 DIZ 112 44.995 14.553 26.771 1.00 20.35
C
HETATM 1575 C4 DIZ 112 45.507 14.004 28.010 1.00 19.96
C
HETATM 1576 C5 DIZ 112 46.522 12.992 27.934 1.00 19.16
C
HETATM 1577 C6 DIZ 112 46.993 12.532 26.669 1.00 19.05
C
HETATM 1578 C7 DIZ 112 44.960 14.431 29.387 1.00 19.88
C
HETATM 1579 C8 DIZ 112 44.482 15.900 29.479 1.00 19.11
C
HETATM 1580 O1 DIZ 112 45.128 16.883 29.170 1.00 19.82
O
HETATM 1581 O2 DIZ 112 43.224 16.042 29.950 1.00 19.25
O
HETATM 1582 N1 DIZ 112 43.871 13.399 29.794 1.00 20.21
N
HETATM 1583 C9 DIZ 112 44.037 12.771 31.037 1.00 19.90
C
HETATM 1584 O3 DIZ 112 44.998 13.033 31.782 1.00 18.53
O
HETATM 1585 C10 DIZ 112 43.086 11.753 31.524 1.00 20.59
C
HETATM 1586 C11 DIZ 112 43.671 10.672 32.209 1.00 21.46
C
HETATM 1587 C12 DIZ 112 42.884 9.636 32.703 1.00 22.62
C
HETATM 1588 I1 DIZ 112 43.831 8.120 33.679 1.00 28.56
I
HETATM 1589 C13 DIZ 112 41.486 9.633 32.527 1.00 21.39
C
HETATM 1590 C14 DIZ 112 40.878 10.720 31.834 1.00 21.18
C
HETATM 1591 C15 DIZ 112 41.675 11.792 31.325 1.00 21.13
C
HETATM 1592 N2 DIZ 112 40.986 12.802 30.650 1.00 20.55
N
HETATM 1593 C16 DIZ 112 41.375 13.473 29.512 1.00 21.76
C
HETATM 1594 O4 DIZ 112 40.624 14.335 29.051 1.00 24.87
O
HETATM 1595 C17 DIZ 112 42.739 13.151 28.806 1.00 21.19
C
HETATM 1596 C18 DIZ 112 42.714 11.792 28.013 1.00 21.92
C
HETATM 1597 C19 DIZ 112 43.911 11.091 27.724 1.00 22.07
C
HETATM 1598 C20 DIZ 112 43.944 9.900 26.994 1.00 22.59
C
HETATM 1599 C21 DIZ 112 42.766 9.364 26.518 1.00 20.71
C
HETATM 1600 CL2 DIZ 112 42.851 7.955 25.617 1.00 21.93
CL
HETATM 1601 C22 DIZ 112 41.529 9.989 26.772 1.00 22.54
C
HETATM 1602 C23 DIZ 112 41.502 11.204 27.521 1.00 22.97
C
END
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Received on Fri Dec 07 2012 - 13:00:02 PST
