[gmx-users] Planar C=C group

David spoel at xray.bmc.uu.se
Thu Feb 12 21:31:01 CET 2004

On Thu, 2004-02-12 at 21:08, Coincon Mathieu wrote:
> Hi,
> I'm making several new residues (in fact ligands covalently bound to one
> residue of my protein)  so I built some building-blocks (new-residus
> entry) in ffG43a1.rtp.
> For the majority it's working well but for one in particular i have a
> problem:
>     I need to keep planar a group of atoms      .._N-Ci=Cj-O-..
> |
> Ck-...
>   The only way I found is to make a new angle entry in the
> ffG43a1bon.itp
> #define ga_47       120.00     2500.00;
> and apply this ange for each angle of my group.
> As you can see my force constant is pretty high.
> Is-it correct ?
> I try a lot of things but wasn't able to keep them planar without my
> ga_47 (even with a gi_1 on N Ci Cj O and/or
> Ck-Ci-Cj-O3 ;  lot's of gd_.. taken from existing or home-made ;
> etc....).
> What can I do?
You want an improper dihedral if this is a ring like system. Putting in
an angle with a high force constant will induce high frequency motions,
and hence you will have to reduce your time step. Moreover, it will not
prevent the groups from going out of the plane. Check ring definitions
in e.g. Phe for an example. 

> Thank you.
> --
> Mathieu Coincon PhD Student
> Universite De Montreal/Departement de biochimie
> Pavillon Roger Gaudry Local D345
> (514).343.6111 #5352
> ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿà›î±ê왨¥Šx%ŠË`›î±êìþ
> 虧,þŠà†ÛiÿÿðÃஉšrÏè®æj)fjåŠËbú?‚lÿºÇ«°ù^jǝ¢í¦‹-þéÿ²æìr¸›z·ª¹ë-²Ú-
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> 虧,þŠà
David van der Spoel, PhD, Assist. 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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