[gmx-users] How to set up dihedrals

Thomas Schlesier schlesi at uni-mainz.de
Thu May 14 13:16:24 CEST 2009

Dear all,
i'm making a .rtp for a sugar for the OPLS-AA force-field. To start i
made a topology with the PRODRG server, so i have a list with all bonds,
angles and dihedrals, but the problem is, that i'm missing the unpolar
hydrogens. How to set up the bonds and angles entrys is no problem, but
with the dihedrals i have problems.

If i have for example the the following molecule (should look like a
double Y):

L1\   /R1
L2/   \R2

(L1 and L2 bounded to L, then L to R, and R is bounded to R1 and R2)
In this case i have the dihedral between L and R, but i have 4
possibilities to set it up:
So my problem is how to choose which possibility should i use. If L1, L2
and R1, R2 are equal there is no problem, because then the 4
possibilities are all equal.

Hope somebody can help me.


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