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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