From: fett_at_vtr.net
Date: Wed Jun 02 2010 - 09:57:09 CDT
Hi:
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.
Best
Jose Antonio
On Wed, 26 May 2010 10:53:39 +0200
ehenriques_at_qui.uc.pt wrote:
> Have a look at
> http://www.ks.uiuc.edu/Training/Tutorials/science/forcefield-tutorial/forcefield-html/
>
> .. 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,
>
> E.
>
> Quoting matziast_at_med.uth.gr:
>
>> Hi,
>> 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.
>> How I can find which parameters are the correct ones?
>> I would appreciate any advice.
>> Thank you in advance.
>> Maria
>>
>>
>
> --
> 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
>
> Tel.: +351 23 9852080 - ext.417
>Fax : +351 23 9827703
>
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