[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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