[gmx-users] Re: Problem with Amber99SB-ILDN ff

[Melchor S.]

I am using gromacs 4.5.5, I didn't  tell you yesterday. I have been tried a
lot of things, but without any success.

One of that I think has to work fine, is with the NGLU nomenclature, but
when I use it, I obtain this
There is a dangling bond at at least one of the terminal ends and the force
field does not provide terminal entries or files. Edit a .n.tdb and/or
.c.tdb file.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I am really sure about the structure of the Ligand ( Glu is in a separate
chain like a ligand) so I don't know what to do.

My PDB file looks like this 

.......
[...]
ATOM   1896  OXT ALA A 258      -5.158  76.455 109.444  1.00 26.88      A     
TER
HETATM 1932  N   NGLU B   1      18.161  74.498 104.017  1.00 24.96    
HETATM 1933  CA  NGLU B   1      18.483  73.747 105.315  1.00 22.94
HETATM 1934  C   NGLU B   1      19.769  73.978 105.618  1.00 27.29
HETATM 1945  O   NGLU B   1      20.258  74.226 106.781  1.00 28.71
HETATM 1936  CB  NGLU B   1      18.262  72.255 105.280  1.00 19.40
HETATM 1937  CG  NGLU B   1      18.556  71.574 106.686  1.00 19.32
HETATM 1938  CD  NGLU B   1      17.462  71.977 107.666  1.00 21.73
HETATM 1939  OE1 NGLU B   1      16.330  72.460 107.490  1.00 22.44
HETATM 1940  OE2 NGLU B   1      17.965  71.816 108.815  1.00 30.0
HETATM 1941  OXT NGLU B   1      20.862  74.195 104.777  1.00 27.10
END    



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