[gmx-users] Question about dihedral angle notation
jalemkul at vt.edu
Sun Dec 2 13:58:34 CET 2012
On 12/1/12 1:54 PM, Andrew DeYoung wrote:
> 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
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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users