[gmx-users] Re: help with "interaction of type atom in the topology"...
klexa
klexa at umich.edu
Fri Aug 31 05:03:41 CEST 2012
>>
If I recall correctly, the residue number printed by pdb2gmx is actually the
residue index (starting from zero), so the problematic residue is MLE, which
does have CB.
-Justin
>>
Hi Justin,
Thank you for the fast response. That makes sense, but the problematic
residue is actually both I guess - I tried just a trimer of
ALA-SAR-ALA, and it chokes, it also fails with the same error for the
trimer of ALA-MLE-ALA, while a different nonstandard amino acid that I
made succeeds as a trimer ALA-ABA-ALA - the major difference perhaps
being the fact that the peptide bond N is methylated for MLE and SAR
but not for ABA that suceeds? This is what MLE looks like:
[ MLE ]
[ atoms ]
N N -0.22670 1
CN CT -0.22340 2
HN1 H 0.10210 3
HN2 H 0.10210 4
HN3 H 0.10210 5
CA CT -0.05180 6
HA H1 0.09220 7
CB CT -0.11020 8
HB2 HC 0.04570 9
HB3 HC 0.04570 10
CG CT 0.35310 11
HG HC -0.03610 12
CD1 CT -0.41210 13
HD11 HC 0.10000 14
HD12 HC 0.10000 15
HD13 HC 0.10000 16
CD2 CT -0.41210 17
HD21 HC 0.10000 18
HD22 HC 0.10000 19
HD23 HC 0.10000 20
C C 0.59730 21
O O -0.56790 22
[ bonds ]
N CN
CN HN1
CN HN2
CN HN3
N CA
CA HA
CA CB
CA C
CB HB2
CB HB3
CB CG
CG HG
CG CD1
CG CD2
CD1 HD11
CD1 HD12
CD1 HD13
CD2 HD21
CD2 HD22
CD2 HD23
C O
-C N
[ impropers ]
-C CA N CN
CA +N C O
MODEL 1
ATOM 1 N ALA A 1 2.847 5.798 -7.887 1.00 0.00 N
ATOM 2 CA ALA A 1 1.622 5.058 -8.157 1.00 0.00 C
ATOM 3 C ALA A 1 1.902 3.942 -9.176 1.00 0.00 C
ATOM 4 O ALA A 1 3.029 3.773 -9.643 1.00 0.00 O
ATOM 5 CB ALA A 1 0.549 6.042 -8.629 1.00 0.00 C
ATOM 6 H ALA A 1 3.680 5.502 -8.376 1.00 0.00 H
ATOM 7 HA ALA A 1 1.214 4.676 -7.221 1.00 0.00 H
ATOM 8 HB1 ALA A 1 -0.375 5.501 -8.835 1.00 0.00 H
ATOM 9 HB2 ALA A 1 0.369 6.785 -7.852 1.00 0.00 H
ATOM 10 HB3 ALA A 1 0.887 6.541 -9.537 1.00 0.00 H
ATOM 11 N MLE A 2 0.814 3.165 -9.517 1.00 0.00 N
ATOM 12 CN MLE A 2 0.967 2.072 -10.481 1.00 0.00 C
ATOM 13 CA MLE A 2 -0.491 3.432 -8.917 1.00 0.00 C
ATOM 14 C MLE A 2 -0.439 3.310 -7.362 1.00 0.00 C
ATOM 15 O MLE A 2 0.107 2.398 -6.778 1.00 0.00 O
ATOM 16 CB MLE A 2 -1.599 2.488 -9.538 1.00 0.00 C
ATOM 17 CG MLE A 2 -2.739 3.173 -10.337 1.00 0.00 C
ATOM 18 CD1 MLE A 2 -3.758 3.767 -9.396 1.00 0.00 C
ATOM 19 CD2 MLE A 2 -2.404 4.282 -11.348 1.00 0.00 C
ATOM 20 HN1 MLE A 2 1.313 2.473 -11.433 1.00 0.00 H
ATOM 21 HN2 MLE A 2 1.696 1.354 -10.103 1.00 0.00 H
ATOM 22 HN3 MLE A 2 0.008 1.575 -10.623 1.00 0.00 H
ATOM 23 HA MLE A 2 -0.732 4.490 -9.025 1.00 0.00 H
ATOM 24 HB2 MLE A 2 -1.134 1.789 -10.233 1.00 0.00 H
ATOM 25 HB3 MLE A 2 -2.093 1.933 -8.740 1.00 0.00 H
ATOM 26 HG MLE A 2 -3.192 2.451 -11.016 1.00 0.00 H
ATOM 27 HD11 MLE A 2 -4.551 4.244 -9.972 1.00 0.00 H
ATOM 28 HD12 MLE A 2 -4.184 2.978 -8.776 1.00 0.00 H
ATOM 29 HD13 MLE A 2 -3.276 4.509 -8.759 1.00 0.00 H
ATOM 30 HD21 MLE A 2 -3.323 4.643 -11.810 1.00 0.00 H
ATOM 31 HD22 MLE A 2 -1.909 5.106 -10.834 1.00 0.00 H
ATOM 32 HD23 MLE A 2 -1.742 3.885 -12.118 1.00 0.00 H
ATOM 33 N ALA A 3 -1.059 4.314 -6.647 1.00 0.00 N
ATOM 34 CA ALA A 3 -1.097 4.341 -5.192 1.00 0.00 C
ATOM 35 C ALA A 3 -1.861 5.587 -4.715 1.00 0.00 C
ATOM 36 O ALA A 3 -2.338 6.389 -5.518 1.00 0.00 O
ATOM 37 CB ALA A 3 0.338 4.283 -4.663 1.00 0.00 C
ATOM 38 H ALA A 3 -1.514 5.074 -7.133 1.00 0.00 H
ATOM 39 HA ALA A 3 -1.536 3.415 -4.821 1.00 0.00 H
ATOM 40 HB1 ALA A 3 0.325 4.303 -3.573 1.00 0.00 H
ATOM 41 HB2 ALA A 3 0.815 3.364 -5.003 1.00 0.00 H
ATOM 42 HB3 ALA A 3 0.898 5.141 -5.034 1.00 0.00 H
TER 43 ALA A 3
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