From: Henriette Elisabeth Autzen (Henriette_at_chem.au.dk)
Date: Tue Jun 14 2011 - 08:33:58 CDT
Dear NAMD users,
I am trying to simulate a protein in NAMD using the OPLS-AA FF. For
this purpose, I have the Charmm formatted OPLS-parameters for proteins
distributed at the Mackerell's homepage
I have a question regarding how the impropers are treated in Charmm and OPLS.
The dihedral potential is modelled using a cosine function in both
Charmm and OPLS so I would expect no problems when NAMD reads the
However, the improper dihedrals are modelled differently using a
harmonic potential in Charmm and a cosine function in OPLS.
In the Charmm formatted OPLS protein file (par_opls_aa.inp) the
impropers are written as if they are modelled by a cosine function,
e.g. for the aromatic ring in phenyl alanine from the par_opls_aa.inp:
H146 C145 C145 C145 1.1 2 180
Can I assume that the OPLS parameters in Charmm format are treated
according to the cosine function and not the harmonic function? If
not, how is planarity enforced using OPLS in NAMD?
Thank you in advance.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:26 CST