On 19/10/2011 3:50 PM, mu xiaojia wrote:
Dear gmx-users,
Does anyone know where can I find any explanations about the atom
names in ffbonded.itp file in oplsaa.ff? I am trying to compare the
amino acids' parameters in gromacs 4.5.4 with in tinker. Or where to
find the default parameters gromacs takes for amino acids in its
aminoacids.rtp file?
For example, it is hard to guess what are C*, C_2 and C= in
ffbonded.itp file:
C* HC 1 0.10800 284512.0 ;
C C3 1 0.15220 265265.6 ; END
C_2 C3 1 0.15220 265265.6 ; END
...
C= C= HC 1 120.000 292.880 ; wlj
C C= HC 1 119.700 292.880 ;
Thanks!
You need to cross-reference the OPLS atom types (full description in
their literature, partial description in atomtypes.atp) with the atom
names in ffnonbonded.itp to make ffbonded.itp more clear.
Mark
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