ygmu at theochem.uni-frankfurt.de
Thu Aug 8 14:33:16 CEST 2002
Here I use oplsaa force field
use residue ACE and NAC to build a NMA molecue (a model of peptide group).
(there are mistakes in ffoplsaa.hdb in NAC unit, just change CA to CH3.)
I found 4 dihedral angle missing they are
CT (ACE) -C -N- CT (NAC),
CT(ACE) - C-N- H (NAC)
O (ACE) - C-N- CT (NAC),
O (ACE) - C-N- H (NAC)
I have checked the ffoplsbon.itp file, there do exists dihedral CT-C-N-CT
type. So I donot understand why it miss CT (ACE) -C -N- CT (NAC) dihedral.
Can you explain me a little how gromacs find dihedrals and pairs ?
And I also find pairs donot contains hydrogen pairs, this also surprise me,
because I think in opls there is a 1,4 electrostatic factor 0.5 , should
also have effects on two-hydrogen pair.
Coudl you explain me how gromacs finish the 1,4 electrostatic reduction ?
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