Date: Wed Jun 02 2010 - 09:57:09 CDT
If you want to keep the the ring in a planar geometry you will need to provide
improper angles, like the ones that are use in the peptidic bond to keep it
plane. As a hint, you should look at the improper bond in residues like
tyrosine or phenilalanine were the aromatic ring is kept rigid by this means.
On Wed, 26 May 2010 10:53:39 +0200
> Have a look at
> .. and you could use residues such as IMD or IME (look in the
> top_all27_prot_lipid_na.inp file) as templates.
> Hope it helps,
> Quoting matziast_at_med.uth.gr:
>> I have a problem and I need someone's help. First of all, I will
>> tell you which
>> is my purpose. I try to create the parameter file of a small
>> molecule in order
>> to run molecular dynamic simulations. Specifically, I have a ring
>> with 5C that
>> has a bending in one side and I want to make flat this ring.I don't know
>> How I can find which parameters are the correct ones?
>> I would appreciate any advice.
>> Thank you in advance.
> Elsa S. Henriques e-mail: ehenriques_at_qui.uc.pt
> Investigadora Auxiliar
> Biologia Estrutural e Computacional (@CNC)
> e Grupo de QuÃmica Estrutural (@CCC)
> Cv15 - RMB Lab
> Departamento de QuÃmica - Universidade de Coimbra
> 3004-535 COIMBRA Portugal
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