[gmx-users] Planar C=C group

[Coincon Mathieu]

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?

Thank you.


--
Mathieu Coincon PhD Student
Universite De Montreal/Departement de biochimie
Pavillon Roger Gaudry Local D345
(514).343.6111 #5352