[gmx-users] improper dihedral description in ARG topology

[David]

On Thu, 2004-05-13 at 17:13, F.Hao at chem.rug.nl wrote:
> Hi, all:
>     In ffG43a*.rtp files, ARG has several improper dihedrals defined.
> Two of them are :    NE    CD    CZ    HE    gi_1
>                      CZ   NH1   NH2    NE    gi_1
> When I generate topology file for ARG, I noticed that these two improper 
> dihedrals were given in sequence as:
> 		     NE    CD    CZ    HE    gi_1 
> 		     NE   NH2   NH1    CZ    gi_1
> So the first were given in the same order as in the rtp file but 
> the second is on the contrary. Although this would not change the 
> dihedrals, I am curious about why the way to output the improper 
> dihedrals are different here. Any hint will be sincerely appreciated. 

>From a vague recollection of when I implemented that, I'd say that it
sorts the atoms such that we can check whether generated proper
dihedrals should be thrown out. As you say the order shouldn't matter...
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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