[gmx-users] Why are there five Urey-Bradley parameters

Lee-Ping leeping at MIT.EDU
Mon Jun 18 17:00:24 CEST 2007


I'm trying to use Urey-Bradley terms in a certain molecule.  If I
understand correctly, the potential function is completely described by
four parameters; for atoms ABC, there is the equilibrium angle ABC, the
harmonic angle constant, the equilibrium distance AC, and the harmonic
stretching constant.

I toggled Urey-Bradley by setting the form of the angle potential
function to "5" under [angles] in my .itp file.  If I include four
parameters, grompp gives me the following:

WARNING 1 [file "testurey.itp", line 65]:
  No default U-B types, using zeroes

This error will not show up if I include five parameters, but what could
this fifth parameter possibly mean?  Thanks a lot.

Here's a snippet of the itp file.

[angles]
    2     1     3     5   1 1 1 1 1; a set of parameters that works
    2     1     4     5        110.06   a_hch   0.1793   u_hch; a set of
parameters that doesn't work (a_hch and u_hch are previously defined)

- Lee-Ping




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