[gmx-users] 11-cis retinal topology problem

Albert mailmd2011 at gmail.com
Sat Jul 6 16:30:21 CEST 2013


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:

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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