[gmx-users] Question about dihedral angle notation

[Justin Lemkul]

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   0.00000  -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
> 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

========================================