[gmx-users] Question about dihedral angle notation

Andrew DeYoung adeyoung at andrew.cmu.edu
Sat Dec 1 19:54:36 CET 2012


I am looking at the file ffbonded.itp located in the oplsaa.ff directory
(usually located in /usr/local/gromacs/share/gromacs/top/oplsaa.ff).  I see
the following entry in the [ dihedraltypes ] section:

  C3     CT     OH     HO      3      0.41840   1.25520   0.00000  -1.67360
0.00000   0.00000 ; Alcohols   with scl14 = 2,2

I have two questions about this entry:

(1) What does the atom type "C3" represent?  "CT" represents a tetrahedral
carbon, "OH" represents an alcohol oxygen, and "HO" represents an alcohol
hydrogen.  But what does "C3" represent?  The paper Cornell et al., J. Am.
Chem. Soc. 1995, 117, 5179-5197 ( located at:
http://pubs.acs.org/doi/abs/10.1021/ja00124a002 ) has a partial list of
AMBER atom type abbreviations on page 5182, but I do not see C3 listed

(2) What does the entry mean when it says "scl14 = 2,2"?  Do you have any
thoughts on this?

Thank you so very much for your time!

Andrew DeYoung
Carnegie Mellon University

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