Re: about diahedra entry in top_all22_sugar.inp

From: Leonardo Trabuco (
Date: Fri Oct 13 2006 - 15:14:58 CDT


On Fri, Oct 13, 2006 at 01:31:35PM -0500, bqluan wrote:
> Dear all,
> I found three entries for each diahedra in top_all22_sugar.inp. For
> examples,
> OHS CBS CTS OHS -4.9362 1 0.0
> OHS CBS CTS OHS 0.2907 2 0.0
> OHS CBS CTS OHS 0.4638 3 0.0
> I am wondering which one NAMD takes in calculations of energy.

All of them. In the same file, you should be able to find something

!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!atom types Kchi n delta

Thus, in this case you have three dihedral entries with three different
multiplicities (n). The potential is the sum of them. IIRC, CHARMM
format requires that they are listed consecutively in the parameter
file, but I don't know if NAMD requires this as well or not.


Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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