[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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