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#30468 07/31/12 11:26 AM
Joined: Jun 2012
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I have used CHARMM-GUI before to generate the input file for MDS.

Since morning, I have been unable to generate any meaningful input and the server CHARMM is showing the following error:

readmol2 warning: skipped unexpected line before @MOLECULE:
0.0555

readmol2 warning: skipped unexpected line before @MOLECULE:
14 N 22.0280 67.7170 43.5400 N.pl3 0 UNK0 -0.3271

readmol2 warning: skipped unexpected line before @MOLECULE:
15 C 23.2960 66.8770 43.2970 C.3 0 UNK0 0.0011

readmol2 warning: skipped unexpected line before @MOLECULE:
16 C 19.7020 69.9690 41.0610 C.ar 0 UNK0 0.0368

readmol2 warning: skipped unexpected line before @MOLECULE:
17 C 20.7460 69.2110 40.4950 C.ar 0 UNK0 -0.0479

readmol2 warning: skipped unexpected line before @MOLECULE:
18 C 21.5340 68.5080 41.3550 C.ar 0 UNK0 -0.0399

readmol2 warning: skipped unexpected line before @MOLECULE:
19 C 21.1890 68.4920 42.7240 C.ar 0 UNK0 0.0298

readmol2 warning: skipped unexpected line before @MOLECULE:
20 C 20.1680 69.3070 43.2310 C.ar 0 UNK0 -0.0399

readmol2 warning: skipped unexpected line before @MOLECULE:
21 C 19.4220 70.0990 42.4510 C.ar 0 UNK0 -0.0479

readmol2 warning: skipped unexpected line before @MOLECULE:
22 C 18.9660 70.7770 40.0900 C.2 0 UNK0 0.2447

readmol2 warning: skipped unexpected line before @MOLECULE:
23 O 19.4690 71.0190 39.0020 O.2 0 UNK0 -0.2702

readmol2 warning: skipped unexpected line before @MOLECULE:
24 N 17.7350 71.0510 40.4290 N.am 1 GLU1 -0.2983

readmol2 warning: skipped unexpected line before @MOLECULE:
25 CA 16.8770 71.9230 39.7150 C.3 1 GLU1 0.1209

readmol2 warning: skipped unexpected line before @MOLECULE:
26 C 16.3970 72.9480 40.5610 C.2 1 GLU1 0.3253

readmol2 warning: skipped unexpected line before @MOLECULE:
27 O 16.2020 72.6260 41.8630 O.2 1 GLU1 -0.2489

readmol2 warning: skipped unexpected line before @MOLECULE:
28 OXT 15.8660 74.1110 40.3620 O.3 1 GLU1 -0.4793

readmol2 warning: skipped unexpected line before @MOLECULE:
29 CB 15.6560 71.1970 39.2590 C.3 1 GLU1 -0.0140

readmol2 warning: skipped unexpected line before @MOLECULE:
30 CG 16.0800 70.3490 37.9050 C.3 1 GLU1 0.0470

readmol2 warning: skipped unexpected line before @MOLECULE:
31 CD 16.2860 70.8980 36.2720 C.2 1 GLU1 0.3048

readmol2 warning: skipped unexpected line before @MOLECULE:
32 OE1 17.5070 70.4130 35.8530 O.2 1 GLU1 -0.2510

readmol2 warning: skipped unexpected line before @MOLECULE:
33 OE2 15.7220 72.1170 36.2360 O.3 1 GLU1 -0.4806

readmol2 warning: skipped unexpected line before @MOLECULE:
34 H 14.3690 65.2360 48.1580 H 0 UNK0 0.1452

readmol2 warning: skipped unexpected line before @MOLECULE:
35 H 14.7540 63.9860 47.1330 H 0 UNK0 0.1452

readmol2 warning: skipped unexpected line before @MOLECULE:
36 H 19.4600 67.6830 48.7760 H 0 UNK0 0.1438

readmol2 warning: skipped unexpected line before @MOLECULE:
37 H 18.4970 66.7470 49.7470 H 0 UNK0 0.1438

readmol2 warning: skipped unexpected line before @MOLECULE:
38 H 20.3140 66.0600 43.4390 H 0 UNK0 0.0849

readmol2 warning: skipped unexpected line before @MOLECULE:
39 H 21.8730 68.2920 45.6880 H 0 UNK0 0.0529

readmol2 warning: skipped unexpected line before @MOLECULE:
40 H 22.4850 66.7170 45.4790 H 0 UNK0 0.0529

readmol2 warning: skipped unexpected line before @MOLECULE:
41 H 23.5200 67.1050 42.2290 H 0 UNK0 0.0428

readmol2 warning: skipped unexpected line before @MOLECULE:
42 H 24.1330 67.0670 44.0080 H 0 UNK0 0.0428

readmol2 warning: skipped unexpected line before @MOLECULE:
43 H 23.1990 65.7920 43.5380 H 0 UNK0 0.0428

readmol2 warning: skipped unexpected line before @MOLECULE:
44 H 20.9400 69.1690 39.4100 H 0 UNK0 0.0626

readmol2 warning: skipped unexpected line before @MOLECULE:
45 H 22.4140 67.9740 40.9590 H 0 UNK0 0.0636

readmol2 warning: skipped unexpected line before @MOLECULE:
46 H 19.9370 69.3260 44.3090 H 0 UNK0 0.0636

readmol2 warning: skipped unexpected line before @MOLECULE:
47 H 18.6710 70.7730 42.8970 H 0 UNK0 0.0626

readmol2 warning: skipped unexpected line before @MOLECULE:
48 H 17.4340 70.5690 41.2760 H 1 GLU1 0.1498

readmol2 warning: skipped unexpected line before @MOLECULE:
49 HA 17.4680 72.3260 38.8600 H 1 GLU1 0.0614

readmol2 warning: skipped unexpected line before @MOLECULE:
50 HXT 15.5430 74.8000 40.9300 H 1 GLU1 0.2951

readmol2 warning: skipped unexpected line before @MOLECULE:
51 HB1 15.2020 70.5580 40.0520 H 1 GLU1 0.0294

readmol2 warning: skipped unexpected line before @MOLECULE:
52 HB2 14.7790 71.8680 39.1000 H 1 GLU1 0.0294

readmol2 warning: skipped unexpected line before @MOLECULE:
53 HG1 17.0390 69.8430 38.1650 H 1 GLU1 0.0378

readmol2 warning: skipped unexpected line before @MOLECULE:
54 HG2 15.3430 69.5140 37.8410 H 1 GLU1 0.0378

readmol2 warning: skipped unexpected line before @MOLECULE:
55 HE2 15.8340 72.4170 35.3410 H 1 GLU1 0.2951

readmol2 ERROR: @BOND before @MOLECULE!

I have used the PDBs from RCSB-1RV1, 3IX9, 3HJ3


Souparno Adhikary,


Trainee,
Centre of Excellence in Bioinformatics,
Bose Institute,
Kolkata
Joined: Jun 2012
Posts: 18
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Posts: 18
And same kind of errors for every PDB I have tried today...


Souparno Adhikary,


Trainee,
Centre of Excellence in Bioinformatics,
Bose Institute,
Kolkata
Joined: Jan 2009
Posts: 161
S
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Posts: 161
Sorry about the trouble. It should be fixed by now. Can you try again and see if it works?

Sunhwan


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