[gmx-users] using the Fourier function for dihedral in the OPLS FF

[Saeed Nasiri]

Dear Justin

I really thanks for your useful help in the last  topic.
I totally changed the method. I copy the oplsaa.ff file in the working
directory
and insert the parameters in the related files.
But I have a problem with dihedral parameters. As far as I know, the opls
force filed used
the Ryckaert-Bell function for dihedral. I used a set of parameters from a
paper in which
used the Fourier function. I insert the parameter of the Fourier function in
the ffbonded.itp file:


;dihedraltypes
;  i    j    k    l   func     coefficients
  HCC    CTT    CSS    HCC     5      0.00000   0.00000   1.33050   0.00000
  HCC    CSS    C22    HCC     5      0.00000   0.00000   1.33050   0.00000
  HCC    C22    C11    H11     5      0.00000   0.00000   1.33050   0.00000

  CTT    CSS    C22    HCC     5      0.00000   0.00000   1.53130   0.00000
  CSS    C22    C11    H11     5      0.00000   0.00000   1.53130   0.00000
  C11    C22    CSS    HCC     5      0.00000   0.00000   1.53130   0.00000
  C22    CSS    CTT    HCC     5      0.00000   0.00000   1.53130   0.00000
  CTT    CSS    C22    C11     5      7.28000  -0.65690   1.16730
0.00000

  CWW    NAA    CRR    NAA     5      0.00000  19.46000   0.00000
0.00000
  CWW    NAA    CRR    HCR     5      0.00000  19.46000   0.00000
0.00000
  C11    NAA    CRR    NAA     5      0.00000  19.46000   0.00000
0.00000
  C11    NAA    CRR    HCR     5      0.00000  19.46000   0.00000
0.00000
  CRR    NAA    CWW    CWW     5      0.00000  12.55000   0.00000
0.00000
  CRR    NAA    CWW    HCW     5      0.00000  12.55000   0.00000
0.00000
  C11    NAA    CWW    CWW     5      0.00000  12.55000   0.00000
0.00000
  C11    NAA    CWW    HCW     5      0.00000  12.55000   0.00000
0.00000
  NAA    CWW    CWW    NAA     5      0.00000  44.98000   0.00000
0.00000
  NAA    CWW    CWW    HCW     5      0.00000  44.98000   0.00000
0.00000
  HCW    CWW    CWW    HCW     5      0.00000  44.98000   0.00000
0.00000
  CWW    NAA    C11    H11     5      0.00000   0.00000   0.51900
0.00000
  CRR    NAA    C11    H11     5      0.00000   0.00000   0.00000
0.00000
  CWW    NAA    C11    C22     5     -7.15350   6.10640   0.79390
0.00000
  CRR    NAA    C11    C22     5     -5.26910   0.00000   0.00000
0.00000
  NAA    C11    C22    CSS     5     -7.47970   3.16420  -1.20260
0.00000
  NAA    C11    C22    HCC     5      0.00000   0.00000   0.36700   0.00000

but the grompp command gives the following errors:


....
ERROR 63 [file topol.top, line 255]:
  No default Ryckaert-Bell. types


ERROR 64 [file topol.top, line 256]:
  No default Ryckaert-Bell. types


ERROR 65 [file topol.top, line 257]:
  No default Ryckaert-Bell. types

Excluding 3 bonded neighbours molecule type 'IL_cat_chain_A'

ERROR 66 [file topol.top, line 270]:
  ERROR: The cut-off length is longer than half the shortest box vector or
  longer than the smallest box diagonal element. Increase the box size or
  decrease rlist.


Removing all charge groups because cutoff-scheme=Verlet

There was 1 note
-------------------------------------------------------


after that I insert the dihedrals in a file (dihedral.itp) and included in
the topol.top file
but the following errors have printed out:



....
ERROR 4 [file topol.top, line 224]:
  No default Fourier Dih. types


ERROR 5 [file dihedral.itp, line 1]:
  Invalid directive dihedral


WARNING 1 [file dihedral.itp, line 6]:
  Too few parameters on line (source file
  /home/nasiri/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 1790)


WARNING 2 [file dihedral.itp, line 7]:
  Too few parameters on line (source file
  /home/nasiri/gromacs-5.1.4/src/gromacs/gmxpreprocess/toppush.c, line 1790)
....




please tell me how to solve this problem.

thanks in advance for your help.