From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Jun 04 2014 - 10:32:46 CDT
I know you said "SUPER rough", but even so, I'm strongly opposed to the
idea of adjusting a radius without the well depth (or adjusting both while
targeting only one value such as an estimated size). Thin ice, there; then
it *might* be more accurate to take a potential for a neutral gold atom
and just add the +1 charge, even though that's also very, very wrong (not
only do the L-J parameters depend strongly on the formal charge, atoms at
the surface of bulk metal have strongly different vdW behavior than
isolated ones).
Also, if the physical system one wants to simulate has Au(3+), doing a
simulation with Au(1+) won't be of much help; they'll behave totally
different.
There simply does not exist an easy solution to the problem at hand. In
the words of one of the top experts in CHARMM ion parametrization:
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=31423#Post31423
What came before in that thread is also somewhat of a sobering read...
Axel's advice is very insightful and thorough - I couldn't possibly
improve upon it.
On 06/03/2014 05:21 PM, Aron Broom wrote:
> I think if you want to do something SUPER rough as you are suggesting with
> an Au1+, you could use existing CHARMM or AMBER forcefields and use Na+ or
> K+ and adjust the VDW coefficient to match some estimate of the size of Au1+.
>
> But keep in mind that in the simple case of classical MD, those atoms are
> just point charges with some VDW radius, which does a poor job of
> representing metal ions, particularly ones that have more complex orbitals
> than a sodium. So really, you'll just be seeing where a big sodium would
> sit on your protein, which will potentially be a lot different than the
> actual case. In fact, if you are thinking of doing that, you'd almost be
> better advised to just do some kind of Poisson-Boltzman calculation of the
> electrostatic surface potential of your protein and see where the negative
> potentials are distributed.
>
> As Axel suggests, you'd need some more complex treatment to get anything
> accurate. Metals are hard.
>
>
>
>
>
> On Tue, Jun 3, 2014 at 4:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
>
>
> On Tue, Jun 3, 2014 at 10:17 PM, Daniel Torrente <xlb608_at_my.utsa.edu
> <mailto:xlb608_at_my.utsa.edu>> wrote:
>
> 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.
>
>
> again, i think a "just give me the force field" kind of approach is
> going to be successful here. there is much more literature and
> fundamental research ahead of you before i would even begin any kind
> of simulation. you first have to understand the chemistry of what you
> are looking at well enough.
>
> that will most likely require some level of ab initio or
> semi-empirical calculation. using a subset of your total system to
> train and benchmark any force field parameter set.
> i would suspect that you still need some form of many-body potential,
> eg. MEAM to represent Au atoms and study their clustering, which
> means you would have to use an MD code that can handle multiple force
> field types at the same time or supports (mechanical or better)
> coupling of codes.
>
> axel.
>
>
> Thanks
>
> Daniel Torrente
>
>
>
>
> On Tue, Jun 3, 2014 at 2:38 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
>
> hi daniel,
>
>
> On Tue, Jun 3, 2014 at 8:31 PM, Daniel Torrente
> <xlb608_at_my.utsa.edu <mailto: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
> <mailto:akohlmey_at_gmail.com> http://goo.gl/1wk0
> College of Science & Technology, Temple University,
> Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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