[gmx-users] pdb2gmx

Yuguang Mu 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).
after pdb2gmx  
(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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