From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Thu Jun 16 2005 - 12:00:05 CDT
I have been reading the recent J Comput Chem paper by Dr. Mackerell (DOI
10.1002/jcc.20082) and am now questioning the mechanism by which 1,4
interactions are included/excluded for proteins in NAMD.
Dr. Mackerell states:
"1,4 Nonbonded interactions, involving atoms separated by three covalent bonds,
do have nonbonded contributions as well as their spatial relationship being
influenced by the internal terms, including the dihedral term. However,
different biomolecular force fields treat the 1,4 nonbond interactions
differently... The all-atom CHARMM biomolecular force fields do not scale the
1,4 terms (scale factor = 1).
With a scale factor of 1, are 1,4 LJ contributions fully included or excluded in
>From the NAMD Tutorial:
When the scaled1-4 exclusion policy is used (as it should with the CHARMM force
field) nonbonded interactions of atoms separated by three bonds (i.e., atoms 1
and 4 in the chain 1-2-3-4) are modifed. Even if the scaling factor for
electrostatics is 1.0 (as it should be for modern CHARMM force fields), special
modified van der Waals parameters are used for 1-4 pairs of atoms for which they
So how does 1,4 scaling work when there is a special set of 1,4 LJ parameters
specified? Will the special parameters be recognized if scaled1-4 is not
Any insight on the standard/best method for specifying the 1,4 interactions in
NAMD using the CHARMM force field, would be appreciated.
Paul R Brenner, P.E.
Graduate Research Assistant
Computer Science and Engineering
The University of Notre Dame
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