[gmx-users] 11-cis retinal topology problem

[Albert]

Hello guys:

   I am building 11-cis-retinal topology these days. Here is what I did:

first of all, I build a small peptide like compound which 
contains:11-cis-retinal connected to the protonated sidechain of LYS, 
ACE and NME capped the N-term and C-term of the LYS respectively. With 
this compound, I upload to paramchem and obtained a ligand.str file.

Second, I merged the information (including BONDS, ANGLES and DIHEDRALS) 
of the ligand.str file into related section in par_all36_cgenff.prm. 
Then I run charmm2gromacs-pvm.py with command:

python charmm2gromacs-pvm.py par_all36_cgenff.prm top_all36_cgenff.rtf

it generate a folder called cgenff-2b7.ff which includes the following 
files:

aminoacids.rtp  ffbonded.itp     forcefield.doc
atomtypes.atp   ffnonbonded.itp  forcefield.itp

I merged the content of above files into gromacs CHARMM36.ff and build a 
topology for 11-cis-retinal into aminoacids.rtp as following. This 
toplogy only contains informations for 11-cis-retinal and protonated LYS:

-------------------------
[ RETK ]
  [ atoms ]
     N    NH1    -0.47    0
     HN    H    0.31    1
     CA    CT1    0.07    2
     HA    HB    0.09    3
     CB    CT2    -0.18    4
     HB1    HA    0.09    5
     HB2    HA    0.09    6
     CG    CT2    -0.18    7
     HG1    HA    0.09    8
     HG2    HA    0.09    9
     CD    CT2    -0.18    10
     HD1    HA    0.09    11
     HD2    HA    0.09    12
     CE    CT2    0.21    13
     HE1    HA    0.05    14
     HE2    HA    0.05    15
     NZ    NH3    -0.832    16
     HZ1    HC    0.42    17
     HZ2    HC    0.42    18
     C    C    0.51    20
     O    O    -0.51    21
     C1    CG301    0.000    22
     C2    CG321    -0.182    23
     C3    CG321    -0.177    24
     C4    CG321    -0.183    25
     C5    CG2DC1    -0.001    26
     C6    CG2DC1    -0.001    27
     C7    CG2DC2    -0.149    28
     C8    CG2DC2    -0.150    29
     C9    CG2DC1    -0.003    30
     C10    CG2DC1    -0.134    31
     C11    CG321    -0.190    32
     C12    CG321    -0.187    33
     C13    CG2D1    -0.005    34
     C14    CG2D1    -0.043    35
     C15    CG324    0.299    36
     C16    CG331    -0.269    37
     C17    CG331  -0.269    38
     C18    CG331  -0.268    39
     C19    CG331  -0.269    40
     C20    CG331  -0.267    41
     H7    HGA4    0.150    42
     H8    HGA4    0.150    43
     H10    HGA4    0.150    44
     H14    HGA4    0.150    45
     H21    HGA2    0.090    46
     H22    HGA2    0.090    47
     H31    HGA2    0.090    48
     H32    HGA2    0.090    49
     H41    HGA2    0.090    50
     H42    HGA2    0.090    51
     H111    HGA2    0.090    52
     H112    HGA2    0.090    53
     H121    HGA2    0.090    54
     H122    HGA2    0.090    55
     H151    HGA2    0.090    56
     H152    HGA2    0.090    57
     H161    HGA3    0.090    58
     H162    HGA3    0.090    59
     H163    HGA3    0.090    60
     H171    HGA3    0.090    61
     H172    HGA3    0.090    62
     H173    HGA3    0.090    63
     H181    HGA3    0.090    64
     H182    HGA3    0.090    65
     H183    HGA3    0.090    66
     H191    HGA3    0.090    67
     H192    HGA3    0.090    68
     H193    HGA3    0.090    69
     H201    HGA3    0.090    70
     H202    HGA3    0.090    71
     H203    HGA3    0.090    72
  [ bonds ]
     CB    CA
     CG    CB
     CD    CG
     CE    CD
     NZ    CE
     N    HN
     N    CA
     C    CA
     C    +N
     CA    HA
     CB    HB1
     CB    HB2
     CG    HG1
     CG    HG2
     CD    HD1
     CD    HD2
     CE    HE1
     CE    HE2
     O    C
     NZ    HZ1
     NZ    HZ2
     NZ    C15
     C1    C2
     C1    C6
     C1    C16
     C1    C17
     C2    C3
     C2    H21
     C2    H22
     C3    C4
     C3    H31
     C3    H32
     C4    C5
     C4    H41
     C4    H42
     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    H111
     C11    H112
     C12    C13
     C12    H121
     C12    H122
     C13    C14
     C13    C20
     C14    C15
     C14    H14
     C15    H151
     C15    H152
     C16    H161
     C16    H162
     C16    H163
     C17    H171
     C17    H172
     C17    H173
     C18    H181
     C18    H182
     C18    H183
     C19    H191
     C19    H192
     C19    H193
     C20    H201
     C20    H202
     C20    H203
  [ impropers ]
     N    -C    CA    HN
     C    CA    +N    O
  [ cmap ]
     -C    N    CA    C    +N
-------------------------


with the new forcefild, I run pdb2gmx:

-------------------------
pdb2gmx -f input.pdb -o gmx.pdb
-------------------------


it finished without any warnings or errors for this step. However, when 
I try to run grompp with command:

-------------------------
grompp_mpi -f em.mdp -c gmx.pdb -p topol.top
-------------------------

it failed with messages:

-------------------------
Program grompp_mpi, VERSION 4.6.2
Source code file: 
/home/albert/Desktop/gromacs-4.6.2/src/kernel/topdirs.c, line: 106
Fatal error:
Invalid angle type 0
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------

Does anybody have any idea what's happening?

thank you very much.

Albert