[gmx-users] Re: help with "interaction of type atom in the topology"...
Mark Abraham
Mark.Abraham at anu.edu.au
Fri Aug 31 05:37:41 CEST 2012
On 31/08/2012 1:03 PM, klexa wrote:
> >>
>
> 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.
Good thought, but the index here starts counting from 1 (and has done so
for at least as far back as 4.5.5), so it really means residue 7.
>
> -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
I think the critical difference here is that you may not be building
hydrogens for MLE in this structure, whereas you were in the SAR example
earlier. Giving your pdb2gmx command lines would perhaps have made
things easier to understand w.r.t. use of -ignh or not. pdb2gmx is
failing at a point consistent with the timing of hydrogen building, but
perhaps I might patch it to be more explicit about that. I'm expecting
that your .hdb entries for some of these new residues refer to CB and
this generates the error. Using pdb2gmx -debug 1, or trying the above
example with -ignh may prove illuminating, also.
Mark
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