Re: amber parameters for congo red

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Jun 19 2008 - 04:07:31 CDT

Dear Shaheen

On Thu, Jun 19, 2008 at 9:19 AM, Shaheen Ahmed
<Shaheen.Ahmed_at_pharm.unige.ch> wrote:
> Dear Michel,
>
> Thanks for your email. I'm already using the GAFF forecefield to parametrize
> congo red, however when I start the minimization and equilibration phase I
> get a strange behavior. The hydrogen of the protonated oxygen of the sulfate
> group (which anyway I don't think should be protonated during the setup?!)

It depends on the pH you're trying to mimic. I assume you're trying to
perform your simulations at physiological pH, so in this case the
sulphonate group sould be deprotonated.

> which is in a reasonable position at the beginning of
> minimization/equilibration gets very close to the neighboring oxygen of the
> sulfate and at some point even seems to "fuse" with that oxygen (I find it
> already strange that at that point the minimization does not stop!) and the
> simulation stops when it comes to the equilibration phase. I tried to
> constrain the position of the atoms in the sulfate group and then the
> equilibration worked fine but as soon as I released the constraint after
> equilibration I observed the same problem as described above. So to me it
> really seems a problem of the paramatrization of the sulfate group in the
> Amber Force Field. Has anybody encountered similar problems with
> parametrizing sulfates with this forcefield? By the way, the input file I
> use for the minimization/equilibration has worked for many other cases and
> for many other ligands. Any help would be highly appreciated.
>

I don't have any experience dealing with sulphonate, but my guess
would be that there are some missing bonding terms between that proton
and the oxygen. This could cause this "fusion" that you observed. Try
to model the ligand with the sulphonate moiety deprotonated and see
what you get.

Cheers,
Michel

> Regards,
>
> Shaheen
>
> L. Michel Espinoza-Fonseca wrote:
>
> Dear Shaheen,
>
> The use of the Generalized Amber Force Field (GAFF) would be useful in
> this case:
>
> http://amber.scripps.edu/antechamber/gaff.html
>
> I hope it helps.
>
> Cheers,
> Michel
>
>
> On Wed, Jun 18, 2008 at 10:29 PM, Shaheen Ahmed
> <Shaheen.Ahmed_at_pharm.unige.ch> wrote:
>
>
> Dear All,
>
> Does anyone know where I could find amber parameters for congo red and/or
> how I should parametrize its sulfate group? Many thanks in advance for your
> help.
>
> Regards,
>
> Shaheen
>
>
>
>
>
>

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