On 12/1/12 1:54 PM, Andrew DeYoung wrote:
Hi,
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 0.0 -1.67360
0.0 0.0 ; 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
there.
Different representations of atom types are used in atomtypes.atp and
ffbonded.itp. The entries in ffnonbonded.itp are sort of a translation between
the two, since there are far fewer bonded types than there are nonbonded types.
The C3 type appears to represent a variety of different situations.
(2) What does the entry mean when it says "scl14 = 2,2"? Do you have any
thoughts on this?
It appears to be some sort of vague notation for 1-4 scaling. I'm afraid I
don't know what it means, either. OPLS has a complex history and I know the
parameters in these files come from many different sources; tracking them down
may be difficult.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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