Re: amber parameters for congo red

From: Shaheen Ahmed (
Date: Thu Jun 19 2008 - 02:19:08 CDT

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?!) 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.



L. Michel Espinoza-Fonseca wrote:
> Dear Shaheen,
> The use of the Generalized Amber Force Field (GAFF) would be useful in
> this case:
> I hope it helps.
> Cheers,
> Michel
> On Wed, Jun 18, 2008 at 10:29 PM, Shaheen Ahmed
> <> 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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