[gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)

[fulya caglar]

    Hi Tsjerk,
      Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain  parameterization briefly.
   
  And I dont think there is a problem with the mail server?Why did you ask?

Thank you very much!!!
  Sincerly
  Fulya

      
---------------------------------
  From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Subject: Re: [gmx-users] Fwd: How can I do the simulation of a protein with
Tyr (SO3H)

Hi Fulya,

You can't just simulate everything you set your mind on. There are no
parameters for sulfite bound tyrosine in the database (just what it
says). You have to add them yourself, which I don't recommend at this
point, since it is clear you have but little experience in this field
(and parameterization is an advanced topic).

By the way, do you have some problems with the mail server?

Best,

Tsjerk

On 3/27/07, fulya caglar wrote:
>
>
> Note: forwarded message attached.
>
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> ---------- Forwarded message ----------
> From: fulya caglar 
> To: Gromacs 
> Date: Tue, 27 Mar 2007 04:45:43 -0700 (PDT)
> Subject: How can I do the simulation of a protein with Tyr (SO3H)
>
> Hi!
> I'm trying to do a simulation of a protein with bound sulfite ion (Tyr
> (SO3H)).After the first command ( pdb2gmx) I am getting the following error
> message :
> -------------------------------------------------------------------------------------------------------------------------------------
> Fatal error:
> Residue 'SUL' not found in residue topology database
> -------------------------------------------------------------------------------------------------------------------------------------
>
> I would be very glad to know why I get this type of error and what can I do
> about this. With thanks
> Sincerely Fulya
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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