Re: Dioxygen atom type with CHARMM36

From: Francesco Pietra (
Date: Wed Nov 12 2014 - 01:17:44 CST

> oxygen is mostly bound to transporters,

Actually, when not remaining bound to humans, there are more oxidases and
oxigenases than dioxygen transporters. And such proteins as cytoglobin and
the marine vs terrestrial neuroglobins perform still unclear roles with
respect to dioxygen. From this viewpoint (although I admit that the
reactions carried out by oxigenases and oxidaes are not covered by
classical MD) an accurate parameterization of aerial dioxygen would be
welcome. However, I understand your point, if the request is low, first
deal with more popular requests.

go uniquely with experimental data {as to O2 params}

is a conclusion from the developer side to be taken seriously. I am not
familiar with GROMACS (although I have compiled it with free ORCA for
QM-MM) but, for the little I know about, params are there strongly bound to
experiments. I have to look there about dioxygen.

Again thank you very much and apologies (if due) for bringing the
discussion to side arguments with respect to the origin of this thread.

francesco pietra

On Tue, Nov 11, 2014 at 9:19 PM, Kenno Vanommeslaeghe <> wrote:

> On 11/11/2014 02:34 PM, Francesco Pietra wrote:
>> QM at which level? In my experience, triplet O2 is such a definitely
>> multireference species that ab initio calculations become a problem,
>> while DFT has no room.
> Good point. Since there's only one bond length and one vibrational mode,
> it's probably better anyhow to scratch the QM and go uniquely with
> experimental data.
> As to the chance of finding problems with proteins involving triplet O2, I
>> would not say it is an uncommon event. Since O2 begun to populate the
>> atmosphere some billion years ago, most organisms, at all taxonomic
>> levels, adapted to it and can't survive without it.
> Be that as it may, people ask us for free oxygen parameters approximately
> once every 2 years, and there's a seemingly infinite list of force field
> improvements that are in higher demand (In this context, I deliberately
> wrote "biological MD systems" rather than "biological systems".) Note that
> heme-bound oxygen is a different story, which is why that species is in
> toppar_all36_prot_heme.str
> Or to put it in "philosophical" (i.e. biological) terms, significant
> levels of free oxygen in the cyptoplasm will cause oxidative damage and
> limit the life span of aerobic organisms; oxygen is mostly bound to
> transporters, and rendering these transporters inoperative at the genetic
> level compromises viability. It's somewhat related to the reason why
> eukaryotes have mitochondria; this way, the oxidative violence is contained
> in a sub-organism with a shorter life cycle than the host cell.

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