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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Mar 27 14:05:16 CEST 2007

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?



On 3/27/07, fulya caglar <fulyacaglar at yahoo.com> wrote:
> Note: forwarded message attached.
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> ---------- Forwarded message ----------
> From: fulya caglar <fulyacaglar at yahoo.com>
> To: Gromacs <gmx-users-request at gromacs.org>
> 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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