[gmx-users] GROMOS (ffG43a2) dihedral potentials

[Dallas Warren]

Roger,

>1) #define gd_3    180.000   7.11    2
>     ;  -C-OA-  (carboxyl)    4.0
>
>2) #define gd_14   0.000     3.77     3
>     ;  -C,CHn, SI-NT,NL,OA (sugar)  3
>
>3) #define gd_8     0.000     2.09     2
>     ;  O-CH1-CHn-O    0.5
>
>In example 1, is it safe to assume that C and OA are the ith (first) and lth
>(fourth) atoms of the four atoms that make up the dihedral angle.  If so,

I think that you will find that it actually means in 1) that it is a 
dihedral defined around the 2 and 3 atoms of the dihedral, C and OA 
respectively.  So it is a chain of X-C-OA-Y and the dihedral is around the 
central bond.  Which makes sense since it is the nature of the atoms on 
either side of the bond that generally dictate how the dihedral around the 
bond will behave.  When there are special cases where the 1 or 4 atom also 
influence it, well that is shown in 3).

>would example 2 be describing a system in which one could have a combination
>of C with NT, NL, or OA; or a combination of CHn with NT, NL, or OA; or a
>combination of SI with NT, NL, or OA.  Does the last example (example 3)

2) to me means C-NT, C-NL, C-OA, CHn-NT ... etc.  "-" indicates a bond, "," 
separates the options/possible atoms that it is applicable to.

>describe a system in which all four atoms of the dihedral are being
>described in that particular order?  Is this a special case where all atoms
>are listed?  Also, in all cases there is a number on the comment line after

3) is a dihedral around a CH1-CHn bond, but there happens to be a O on 
either end.  So if there happens to also be a general CH1-CHn or some 
variation somewhere else defined, but you have O-CH1-CHn-O in your 
molecule, then use 3) instead as it is a special case.

>the atom types:  Example 1 - 4.0, Example 2 - 3, and Example 3 - 0.5.  What
>do these numbers represent?

No idea, haven't been able to work that one out.  It is a comment only and 
may come from GROMOS as a note or something?

Catch ya,

Dr. Dallas Warren
Research Fellow
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9083
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