[gmx-users] hand made rtp entry: grompp doesn't find the dihedral parameters i included explicitly

Michael Brunsteiner mbx0009 at yahoo.com
Sun Nov 6 15:02:12 CET 2005

Dear all,

I made myself an additional entry for an organic
molecule in ffoplsaa.rtp. I use existing atom types
from opls-aa and everything works fine with additional 
explicit bonds/angle parameters i included to the rtp entry. 
however, for some of the proper dihedrals grompp complains:

"No default Ryckaert-Bell. types, using zeroes"
although I DID include these parameters explicitely
in the rtp entry.

what i did was:
1) look up a similar dihedral angle in the existing opls-aa
2) put a #define statement into ffoplsaabon.rtp, as in:
   "#define dih_my_parameters"   followed by the six numbers
   i got from that similar angle
3) include a "[ dihedrals ]" section into the rtp entry
   with a line starting with the 4 atom names followed by
   the keyword "dih_my_parameters"
4) after pdb2gmx i obtain a topol.top file that does
   include this angle followed by the word "dih_my_parameters"
   which is what i expected, however, when using this topol.top
   file with grompp i still get the abovementioned warning(s)

what am i missing ? is there somnething hard-coded here ??

i also tried to include the paramters directly 
into the ffoplsaabon.itp file but grompp wouldn't find them,
e.g., i have a bond between two atom-types that correspond
to the bond-types CA and CV.
if i include a corresponding line into the "[ bondtypes ]" section
of ffoplsaabon.itp, using force constant and bondlength from a 
similar bond in an AA, grompp keeps complaining about not finding
parameters for this bond.

i also found that some (not all) of the dihedrals grompp is missing
should actually be there since they are covered by definitions
including wild cards, such as X CA CA X, in ffoplsaabon.rtp.
grompp would not find them either ...

thanks in advance for any help!


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