Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Susmita/Rajib]

And finally, Dr. Timofey Tyugashev, who was the first to post his
response to my query, perhaps put in a comma between "Bond" and
"Dissociation" in the subject head, "[PyMOL] Is it possible in Pymol
to determine Individual Bond, Dissociation Energy for any Bond in
organic molecules?" which changed the meaning of my requirement
somewhat.

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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Susmita/Rajib]

[Quote]
On 02/06/2017, Osvaldo Martin  wrote:
...send me a private message if you want further details on
this topic ...[/Quote]
Sir, I wouldn't want to waste your precious time!
Not chemical reaction per se, Sir, but only Bond Dissociation Energies
of individual bonds breaking and bonds forming ... emphasis, individually!

[Quote]
On 02/06/2017, Tsjerk Wassenaar  wrote:
... Pymol reads... positions from a coordinate file ... and draw those
...[/Quote]
Understood, Sir, finally!
Then please do advise me on my need I wrote above in reply to Dr.
Martin's email.

...

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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Tsjerk Wassenaar]

Dear Rajib,

Pymol reads atom labels and positions from a coordinate file. It then
determines which atoms are bonded based on distance criteria. That is used
to draw the molecule.
Pymol also has an internal library of molecules and fragments, with atoms
and bonds, which can be used to build bigger molecules.

QM methods are required to determine an optimal molecular geometry. But
that's not something Pymol does. Just read in coordinates and draw those.

Hope it helps,

Tsjerk

On Jun 1, 2017 21:27, "Susmita/Rajib"  wrote:

> No, Dr. Wassenaar, Sir! People have confused me. After two years, I am
> told that:
> [Quote]PyMol does not use QM methods. It also does not "determine the
> structures of molecules" [/Quote]
> I need my illustrious peers to clarify me regarding all my queries in
> all my posts in the present thread.
>
> 
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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Osvaldo Martin]

Hi Rajib,

Probably part of the confusion is due to the meaning of "determine the
structure". I understand "determine" can have different meaning in
different contexts. In my area of research "determine" generally means to
use experimental methods like X-ray crystallography or NMR to establish the
structure of a molecule.

What PyMOL does is to "guess" the topology of a molecule based on some
"chemical rules", distance cutoff and information in files (like Cartesian
coordinate of atoms in PDB files). There is no QM method involved in any
part of the procedure not even semi-empirical or classical force-fields.

If you want to study chemical reaction, theoretically, you need to use QM
methods, and PyMOL is not the software for that.


Please feel free to send me a private message if you want further details
on this topic.

Best,
Osvaldo.


On Thu, Jun 1, 2017 at 9:26 PM, Susmita/Rajib  wrote:

> No, Dr. Wassenaar, Sir! People have confused me. After two years, I am
> told that:
> [Quote]PyMol does not use QM methods. It also does not "determine the
> structures of molecules" [/Quote]
> I need my illustrious peers to clarify me regarding all my queries in
> all my posts in the present thread.
>
> 
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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Susmita/Rajib]

No, Dr. Wassenaar, Sir! People have confused me. After two years, I am
told that:
[Quote]PyMol does not use QM methods. It also does not "determine the
structures of molecules" [/Quote]
I need my illustrious peers to clarify me regarding all my queries in
all my posts in the present thread.

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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Tsjerk Wassenaar]

Hi Rajib,

The bonds are determined based on a distance cutoff.

Hope it helps,

Tsjerk


On Jun 1, 2017 21:15, "Susmita/Rajib"  wrote:

How come we see structures of molecules in PyMol?
https://en.wikipedia.org/wiki/PyMOL


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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Susmita/Rajib]

How come we see structures of molecules in PyMol?
https://en.wikipedia.org/wiki/PyMOL

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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[David Hall]

PyMol does not use QM methods. It also does not "determine the structures of 
molecules".

-David

> On Jun 1, 2017, at 12:38 AM, Susmita/Rajib  wrote:
> 
> Thank you, Dr. Tyugashev, for replying to my query.
> Doesn't PyMol also use those QM methods to determine the structures of
> molecules?
> Then why not PyMol be capable of yielding such values for individual bonds?
> 
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Re: [PyMOL] Is it possible in Pymol to determine Individual Bond, Dissociation Energy for any Bond in organic molecules?

[Susmita/Rajib]

Thank you, Dr. Tyugashev, for replying to my query.
Doesn't PyMol also use those QM methods to determine the structures of
molecules?
Then why not PyMol be capable of yielding such values for individual bonds?

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[PyMOL] Is it possible in Pymol to determine Individual Bond Dissociation Energy for any Bond in organic molecules?

[Susmita/Rajib]

Hello, Illustrious Members!
I have a query:
Let us assume one is in possession of a particular named organic reaction.
In that reaction a set of reactants change into a set of products.
It is very easy to observe in those named reactions as to which bonds
have broken down to form other newer bonds.
Is it possible in Pymol to determine Individual Bond Dissociation
Energy for any such Bond of those reactants and products?
Regards

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