[gmx-users] bond angles and (improper) dihedrals angles in PRODRG

hugo verli hugo at acd.ufrj.br
Tue Aug 13 16:13:25 CEST 2002

Hi to all,

in the PRODRG paper (J.Comp.Aid.Mol.Des., 1996, 10, 255-262) it is shown that
bond, angle, improper dihedral angle and dihedral angle for a given molecule are
defined based on a GROMOS forcefield list containing information about optimal
distances, optimal angles and force constants. Were the terms on this parameter
list modified in GROMACS forcefield? How can I obtain this list?

Further in the same paper, it is told that if does not exist a previous
information about a certain combination of atoms in a bond or angle, the nearest
plausible code is selected, and the user will be warned if such case occur.

This warning is implemented in PRODRG Server? 

I apologize if I missed something in the manual, the paper and/or the algorithm. 
But I became curious about some c1 values (improper dihedrals) in .top file (I
think that it is a constant k in equation 4.51, pag. 57, of GROMCAS manual, it
is right?), 1673.6 and 836.8, one the half of the other.

Thanks is advance for any coment,

Hugo Verli.

More information about the gromacs.org_gmx-users mailing list