[gmx-users] 11-cis retinal topology problem

[Albert]

On 07/07/2013 10:23 AM, Mark Abraham wrote:
> Program grompp, VERSION 4.6.3
> >Source code file:
> >kernel/topdirs.c, line: 106
> >


Hello Mark:

  thanks a lot for kind reply. Do you mean the above information? I open 
this file and here is the line 106:

gmx_fatal(FARGS, "Invalid angle type %d", type);


here is the angetypes section in the ffbonded.itp file which generated 
from the python scrips, to be honest I don't see anything bad....

thank you very much.

Albert



[ angletypes ]
; i    j    k    func    th0    cth    ub0    cub
CT2    CT2    NCH1    5    111.20    669.44    0.0    0.0
HCR    NCH1    CT2    5    118.40    292.88    0.0    0.0
CT2    NCH1    CR15    5    123.20    418.4    0.0    0.0
CR15    NCH1    HCR    5    120.00    292.88    0.0    0.0
HA    CT2    NCH1    5    109.50    418.4    0.0    0.0
NCH1    CR15    HPL1    5    119.10    292.88    0.0    0.0
NCH1    CR15    CR14    5    122.90    794.96    0.0    0.0
CR15    CR14    HPL    5    119.70    292.88    0.0    0.0
CR14    CR15    HPL1    5    119.70    292.88    0.0    0.0
CR15    CR14    CR13    5    122.90    794.96    0.0    0.0
CR14    CR13    CT3    5    119.70    585.76    0.0    0.0
CR13    CR14    HPL    5    119.70    292.88    0.0    0.0
CR13    CT3    HA    5    109.50    418.4    0.0    0.0
CR14    CR13    CR12    5    122.90    794.96    0.0    0.0
CR13    CR12    HPL    5    119.70    292.88    0.0    0.0
CR12    CR13    CT3    5    119.70    585.76    0.0    0.0
CR13    CR12    CR11    5    122.90    794.96    0.0    0.0
CR12    CR11    HPL    5    119.70    292.88    0.0    0.0
CR11    CR12    HPL    5    119.70    292.88    0.0    0.0
CR12    CR11    CR10    5    122.90    794.96    0.0    0.0
CR11    CR10    HPL    5    119.70    292.88    0.0    0.0
CR10    CR11    HPL    5    119.70    292.88    0.0    0.0
CR11    CR10    CR9    5    122.90    794.96    0.0    0.0
CR10    CR9    CT3    5    119.70    585.76    0.0    0.0
CR9    CT3    HA    5    109.50    418.4    0.0    0.0
CR9    CR10    HPL    5    119.70    292.88    0.0    0.0
CR10    CR9    CR8    5    122.90    794.96    0.0    0.0
CR9    CR8    HPL    5    119.70    292.88    0.0    0.0
CR8    CR9    CT3    5    119.70    585.76    0.0    0.0
CR9    CR8    CR7    5    122.90    794.96    0.0    0.0
CR8    CR7    HPL    5    119.70    292.88    0.0    0.0
CR7    CR8    HPL    5    119.70    292.88    0.0    0.0
CR8    CR7    CR6    5    122.90    794.96    0.0    0.0
CR7    CR6    CT3    5    119.70    585.76    0.0    0.0
CR6    CR7    HPL    5    119.70    292.88    0.0    0.0
CR7    CR6    CR5    5    122.90    794.96    0.0    0.0
CR6    CR5    CT3    5    119.70    585.76    0.0    0.0
CR6    CR5    CT2    5    119.70    585.76    0.0    0.0
CT3    CR5    CT2    5    119.70    585.76    0.0    0.0
CR5    CT2    HA    5    109.50    418.4    0.0    0.0
CR5    CT3    HA    5    109.50    418.4    0.0    0.0
CR6    CT3    CT2    5    111.10    527.184    0.0    0.0
CR6    CT3    CT3    5    111.10    527.184    0.0    0.0
CR5    CT2    CT2    5    111.10    527.184    0.0    0.0
CR5    CR6    CT3    5    119.70    585.76    0.0    0.0
CT3    CT3    CT3    5    109.50    527.184    0.0    0.0
CT2    CT3    CT3    5    109.50    527.184    0.0    0.0