From: Daniel Torrente (xlb608_at_my.utsa.edu)
Date: Tue Jun 03 2014 - 15:17:15 CDT
Thanks for your quick response
I will take your advice and keep looking for published literature on this
topic. In the mean time, if I tried to use Au+ or Au instead of Au3+, is
there any ff available that could help to carried out this simulation?.
Basically, I do not want to fix the Au atom. I want them to move freely
during the simulation and see the aggregation pattern over the surface of
the protein.
Thanks
Daniel Torrente
On Tue, Jun 3, 2014 at 2:38 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> hi daniel,
>
>
> On Tue, Jun 3, 2014 at 8:31 PM, Daniel Torrente <xlb608_at_my.utsa.edu>
> wrote:
>
>> Hi guys,
>>
>> Is there any available force field that can simulated the interaction
>> between Au+3 and a protein? I was looking for some information in articles
>> and the mailing list related to this topics, but all I could find was the
>> GoiP and GoiP-charmm (immobile surface Au). Also found the charmm-metal ff
>> but it seems that only works with the metal Au and not with the ion Au+3
>> (there is no information in the ff about Au+3).
>>
>> Any suggestion on how to approach this type of interaction? or or could I
>> do this with any of the ff that I mentioned before?
>>
>
> multiply charged ions are very problematic for pair-wise additive force
> fields as their interactions usually include polarization of the immediate
> environment with charge redistribution and directional interactions. most
> likely you will not have a "naked" au3+ cation, but some kind of complex
> with nulcleophilic molecules and/or anions. depending of what you want to
> study, you may need to resolve to doing QM/MM calculations, or
> parameterize an au3+ complex that you keep rigid or otherwise maintain its
> charge distribution.
>
> interactions with gold surfaces are a different system, since those are
> usually dominated by a mostly covalent bond (via sulphur or oxygen) and the
> effects due to polarization of the metal are smaller than other errors of
> the model to be justifiably ignored. often people use rather crude models
> for it, since they don't care as much about the interaction with the gold
> surface than of the objects attached to the surface with each other and the
> items around it.
>
> i suggest you have another look at the published literature and think
> carefully what it is that you really want to learn from your simulations
> and come back, if you still have questions.
>
> also, please don't just take a single opinion on the subject as your
> guideline. for anything this problematic, you have to look at multiple
> contrasting opinions and form your own opinion as there is no single simple
> answer that answers all problems.
>
> axel.
>
>
>
>
>> Thanks in advance
>>
>> Daniel Torrente
>>
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
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