[gmx-users] improper dihedral description in ARG topology
spoel at xray.bmc.uu.se
Thu May 13 20:54:10 CEST 2004
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 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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