[gmx-users] 11-cis retinal topology problem

Mark Abraham mark.j.abraham at gmail.com
Sat Jul 6 22:17:11 CEST 2013


On Sat, Jul 6, 2013 at 4:30 PM, Albert <mailmd2011 at gmail.com> wrote:
> On 07/06/2013 12:14 PM, Mark Abraham wrote:
>>
>> My bad. Use
>>
>> warning_note(wi, "Debugging");
>
>
>
> thanks a lot Mark. I've obtained some informations now:

That's a completely different output. I think both your executables
are broken, somehow. Clean the build and install trees and try again
:-)

Mark

> Identified residue MET1 as a starting terminus.
> Warning: Residue RETK296 in chain has different type (Other) from starting
> residue MET1 (Protein).
> Warning: Residue THR297 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue SER298 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue ALA299 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> Warning: Residue VAL300 in chain has different type (Protein) from starting
> residue MET1 (Protein).
> More than 5 unidentified residues at end of chain - disabling further
> warnings.
> Identified residue ALA295 as a ending terminus.
> 8 out of 8 lines of specbond.dat converted successfully
> Special Atom Distance matrix:
> Fatal error:
> Residue 1 named LEU of a molecule in the input file was mapped
> to an entry in the topology database, but the atom N used in
> an interaction of type improper in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> "History has expired" (PubMed Central)
>
>
>
> I take 11-cis-retinal SCHIFF base charmm format topology from the
> publication (Biophysical Journal, 83:3097-3112, 2002) from here:
>
> http://www.ks.uiuc.edu/Research/namd/wiki/?ParameterTopologyRepository
>
>  and convert into gromacs .itp format:
>
> ; PROTONATED SCHIFF BASE
> [ RETK ]
>  [ atoms ]
>     N    NH1    -0.47000    0
>     HN    H    0.31000    1
>     CA    CT1    0.07000    2
>     HA    HB    0.09000    3
>     C    C    0.51000    4
>     O    O    -0.51000    5
>     CB    CT2    -0.18000    6
>     HB1    HA    0.09000    7
>     HB2    HA    0.09000    8
>     CG    CT2    -0.18000    9
>     HG1    HA    0.09000    10
>     HG2    HA    0.09000    11
>     CD    CT2    -0.18000    12
>     HD1    HA    0.09000    13
>     HD2    HA    0.09000    14
>     CE    CT2    0.340    15
>     HE1    HA    0.050    16
>     HE2    HA    0.050    17
>     N16    NCH1    -0.727    18
>     H16    HCR    0.505    19
>     C15    CR15    0.362    20
>     H15    HPL1    0.189    21
>     C14    CR14    -0.180    22
>     H14    HPL    0.180    23
>     C13    CR13    0.131    24
>     C20    CT3    -0.170    25
>     H20A    HA    0.090    26
>     H20B    HA    0.090    27
>     H20C    HA    0.090    28
>     C12    CR12    -0.110    29
>     H12    HPL    0.110    30
>     C11    CR11    -0.090    31
>     H11    HPL    0.090    32
>     C10    CR10    -0.100    33
>     H10    HPL    0.100    34
>     C9    CR9    0.00    35
>     C19    CT3    -0.27    36
>     H19A    HA    0.09    37
>     H19B    HA    0.09    38
>     H19C    HA    0.09    39
>     C8    CR8    -0.10    40
>     H8    HPL    0.10    41
>     C7    CR7    -0.10    42
>     H7    HPL    0.10    43
>     C6    CR6    0.00    44
>     C5    CR5    0.00    45
>     C18    CT3    -0.27    46
>     H18A    HA    0.09    47
>     H18B    HA    0.09    48
>     H18C    HA    0.09    49
>     C4    CT2    -0.20    50
>     H4A    HA    0.10    51
>     H4B    HA    0.10    52
>     C3    CT2    -0.20    53
>     H3A    HA    0.10    54
>     H3B    HA    0.10    55
>     C2    CT2    -0.20    56
>     H2A    HA    0.10    57
>     H2B    HA    0.10    58
>     C1    CT3    0.00    59
>     C16    CT3    -0.27    60
>     H16A    HA    0.09    61
>     H16B    HA    0.09    62
>     H16C    HA    0.09    63
>     C17    CT3    -0.27    64
>     H17A    HA    0.09    65
>     H17B    HA    0.09    66
>     H17C    HA    0.09    67
>
>  [ bonds ]
>     CB    CA
>     CG    CB
>     CD    CG
>     CE    CD
>     N16    CE
>     N    HN
>     N    CA
>     O    C
>
>     C    CA
>     C    +N
>     CA    HA
>     CB    HB1
>     CB    HB2
>     CG    HG1
>     CG    HG2
>     CD    HD1
>     CD    HD2
>     CE    HE1
>     CE    HE2
>     C1    C2
>     C1    C6
>     C1    C16
>     C1    C17
>     C2    C3
>     C2    H2A
>     C2    H2B
>     C3    C4
>     C3    H3A
>     C3    H3B
>     C4    C5
>     C4    H4A
>     C4    H4B
>
>     C5    C6
>     C5    C18
>     C6    C7
>     C7    C8
>     C7    H7
>     C8    C9
>     C8    H8
>     C9    C10
>     C9    C19
>     C10    C11
>     C10    H10
>     C11    C12
>     C11    H11
>     C12    C13
>     C12    H12
>     C13    C14
>     C13    C20
>     C14    C15
>     C14    H14
>     C15    N16
>     C15    H15
>     N16    H16
>     C16    H16A
>     C16    H16B
>     C16    H16C
>     C17    H17A
>     C17    H17B
>     C17    H17C
>     C18    H18A
>     C18    H18B
>     C18    H18C
>     C19    H19A
>     C19    H19B
>     C19    H19C
>     C20    H20A
>     C20    H20B
>     C20    H20C
>
>  [ impropers ]
>     N    -C    CA    HN
>     C    CA    +N    O
>     C5    C6    C4    C18
>     C6    C1    C5    C7
>     C7    C8    C6    H7
>     C8    C7    C9    H8
>     C9    C10    C8    C19
>     C10    C9    C11    H10
>     C11    C12    C10    H11
>     C12    C11    C13    H12
>     C13    C14    C12    C20
>     C14    C13    C15    H14
>     C15    N16    C14    H15
>     N16    CE    C15    H16
>
> Then I add this information into the aminoacide.rtp file. I don't know why
> it failed. It is expected to be treated as regular amino acid residue....
>
> thank you very much.
>
>
> Albert
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