VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Dec 14 2014 - 03:26:50 CST

To my previous comment as to the usefulness of params for TM complexes, I
should remember - as anyone knows - that it is extremely difficult - if not
impossible - to reach a real minimum during a DFT optimization without
constraints to any atom. In very largely most cases, a minimum is observed
with conformation very distant from the crystal situation. Usually, people
do that optimization by constraining the CA atom of the various aa, thereby
getting some negative vibrational frequencies. And often observing
translationals far from zero. I.e, a mess. So, MD with TM metals
coordinated to the protein can be useful to certain purposes, but rarely
possible at the minimum of sound science.

Could MD, instead of requesting specific bond constants, utilize the normal
mode analysis? I don't know if it could, and how to do that, but it could
make life easier. MD is capable of giving the normal modes from
fluctuations, why not accepting the reverse? Or this is one of my daily
follies.

francesco

On Sun, Dec 14, 2014 at 1:54 AM, zoran <zmatovic_at_kg.ac.rs> wrote:
>
>
> have it whatever way you want. i personally find it is a rather
> unusual approach to ask for help by overtly antagonizing people.
> but if you believe that this is the way that things should work, don't
> let me stop you.
>
>
> I do not know what are you talking about really but I feel the need to
> answer you and that will be my last: I don't remember when I was last time
> offensive toward others - it is not my style - and therefore I behaved the
> same in my post about fftk.
> Major part of my research I am doing in experimental chemistry and try to
> give my best to complete it with computational chemistry.
>
> And you know what, may be looks like a joke for you, but I'll see what I
> can do with a gap between classical ff and TM.
>
> with my best regards
> zoran
>
>
>
> axel.
>
>
>> Thanks for critical discussion Francesco.
>>
>> ZDM
>>
>> While I obviously agree with Axel about the basic science illustrated,
>> there
>> are situations where such dirty parameterizations of transition metal
>> clusters for classical MD prove useful. That is the case when the focus is
>> not the metal complex, while conservation of the geometry of the metal
>> complex during MD is what matters. A case in point is PNAS ͉ August 14,
>> 2007
>> ͉ vol. 104 ͉ no. 33 ͉ 13319 –13324 If you read the PhD thesis behind that,
>> you see that that work was carried out with those limitations in mind. In
>> my
>> view it proved useful. Consequently, tools to develop params for tm
>> complexes may have their interest. Such as the MCPB toolkit in amber
>> quarters, if it goes beyond Zn. cheers francesco pietra
>>
>>
>> On Sat, Dec 13, 2014 at 10:15 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> wrote:
>>
>>>
>>> can't let this go uncommented...
>>>
>>> On Sat, Dec 13, 2014 at 7:50 AM, zoran <zmatovic_at_kg.ac.rs> wrote:
>>>
>>> [...]
>>>
>>> > I am very sorry that scientists making force fields for macromolecules
>>> > forget on transition metals (in general) and that TM make a substantial
>>> > part
>>> > of biological processes.
>>>
>>> if you knew a bit more about force fields and the chemistry of
>>> transition metals, you wouldn't make such a general attack. people
>>> don't do parameters for transition metals for classical (pairwise
>>> additive) force fields, because it is pretty damn near impossible to
>>> get them right. already divalent cations are a big stretch in most
>>> cases and rarely represented well. force fields are always a
>>> compromise, but in the case of transition metals, you have to deal
>>> with the problem of having to describe interactions that have
>>> substantial directional and manybody character (i.e. the interaction
>>> of the transition metal depends on how many and what neighbors are
>>> where) with a spherical functional form. of course, you can follow the
>>> recipe for force fields and derive some parameters, but in most cases,
>>> the resulting simulations are a waste of time. considering the fact
>>> that many force field users are very uncritical about how to use
>>> parameterizations, it is quite understandable, that people, who
>>> specialize in force field parameters, do not want to lead people down
>>> that road and rather not generate and publish sub-standard parameters.
>>>
>>> if you know a way how to do these parameterizations so they are
>>> producing meaningful calculations, please don't hold back and let us
>>> know. we most certainly do not need people that blame everybody else
>>> but themselves.
>>>
>>> axel.
>>>
>>>
>>> > With my best regards to all of you
>>> > Zoran
>>> >
>>>
>>>
>>>
>>> --
>>> 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.
>>>
>>>
>>
>
>
> --
> 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.
>