[gmx-users] Question about dihedral angle notation
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!
Carnegie Mellon University
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