[gmx-users] dihedral parameters in oplsaa

[David van der Spoel]

friendli wrote:
> Hi gmx users,
> 
> In order to understand the oplsaa all atom force field, I use pdb2gmx to 
> generate topology file of a pdb which contains only one AA( the glycine).
> 
> After the EM simulation, I use gmxdump to look for the details of the 
> parameters.
> 
> I find,
> in .top file, there are 15 proper dihedrals under directive [dihedrals] 
> and the funtion type is 3 (i.e. RB dihedrals).
> However, in the output generated by gmxdump, there are explicit 
> parameters for only 9 of these dihedrals.  The 9 dihedrals corresponds 
> to 9 of the 15 in .top correctly, but the other 6 are missing.
> 
> In the six missed dihedrals,  two are for N-CA-C-O, four are for  
> HA-CA-C-O.
> 
> Can anybody give a hint on this? Is there any default value not output 
> by gmxdump? All other parameters are fully printed.
> 
> 
>     H   H  O
>      |    |    | H- N - C - C = O
>      |
>     H

multiple dihedrals share the same parameters. look further down at RBDIHS.
> 
> thank you
> 
> LQ
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se