Jmol 11.9.2 (http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip)
introduces a calculation for molecular volume. This calculation depends
upon what set of Van Der Waals radii one uses. "type" can be one of "Jmol",
"Babel", "Rasmol" or "User". If not provided, "type" defaults to the default
type specified by the command <b>set defaultVanDerWaal</b>. The calculation
is a simple one that just adds up all the Van Der Waals volumes and
subtracts off the overlap of spheres associated with bonds as described by
A. Bondi (<b>J. Phys. Chem. 68, 1964, 441-451.</b>). The built-in Van der
Waals set "Babel" most closely represents this setting.
load c6h6.smol;set defaultVDW babel;
print "" + {1.1}.volume()
print "" + {1.1}.volume("Babel")
print "" + {1.1}.volume("Jmol")'
print "" + {1.1}.volume("Rasmol")
see also http://cehmapps.stolaf.edu/jmol/docs/examples-11/new.htm
Bob
On Wed, Sep 2, 2009 at 7:10 PM, Robert Hanson <[email protected]> wrote:
> Dave, attached is a final script for you. Just run it, and after that you
> can run
>
> print calcVolume()
>
> for any structure you load. Needs testing.
>
> Bob
>
>
>
> On Wed, Sep 2, 2009 at 3:09 PM, Robert Hanson <[email protected]> wrote:
>
>> Sorry, I shouldn't have been so critical. Table 3 has some pretty major
>> differences for aromatics. In the paper they describe multiple approximation
>> methods and then point out that different programs that do the actual
>> molecular volume calculation (as Jmol is doing) produce different results.
>> They hypothesize that these different results are due to different settings
>> for VDW radii without really checking it out. When they reparameterize they
>> get better results, but as far as I can tell it is totally ad hoc.
>>
>> I would say that Jmol, when loaded with the same VDW radii using, for
>> example:
>>
>> load xxxxx.mol
>> {carbon}.vdw = 1.7
>> {oxygen}.vdw = 1.52
>>
>> gives the same result as their MacroModel values (Tran). I don't see any
>> point in comparing values to "TSAR" program without first asking for what
>> they use for VDW radii -- if any program is giving different values, that's
>> almost certainly all there is to it.
>>
>> I only have a few of these models on hand, but here is what I get:
>>
>>
>> compound Bindi Abraham Jmol (isosurface
>> volume resolution 20 sasurface 0)
>>
>> benzene 80.3 95.9 82.7
>> chloromethane 42.0 41.1 42.3
>> cyclohexane 102.0 103.8 101.7
>> testosterone 292.7 309.4 293.6
>> (resolution 15)
>>
>> So, except for the aromatics, that's pretty good. I apologize!
>>
>> OK, so the benefit of the calculation they do is that you don't need a
>> structure. Just a molecular formula and some knowledge about the number of
>> aromatic rings. With Jmol, we have structures. So the first thing I would
>> say is that there's little point in approximating this way; we can do
>> better. Obviously it shouldn't take an isosurface calculation to do this. I
>> think you could get an exact value using a simple Jmol script. It's just a
>> simple analytical calculation.
>>
>> Let me see if I can write that....
>>
>>
>> Bob
>>
>>
>>
>>
>> On Wed, Sep 2, 2009 at 2:25 PM, N David Brown <[email protected]>wrote:
>>
>>> 10-20%? Where's that from, Bob?
>>>
>>> Egon, there are two sets of values compared; one is TSAR, a QSAR
>>> package (I'm just quoting here). The other is values from MacroModel.
>>> Example values are methanol is approximated to 35 instead of 37, while
>>> N((CH2)3CH3)4BPh4 is 592 vs 609. That latter value is the max
>>> difference listed for the MacroModel program.
>>>
>>> David
>>>
>>>
>>>
>>> 2009/9/2 Robert Hanson <[email protected]>:
>>> > Sorry, it just seems to me that 10-20% error is not very good for such
>>> a
>>> > simple calculation. (Just comparing their two methods.) I think these
>>> > people back in 2003 just didn't have suitable resources. It's not like
>>> it's
>>> > that difficult a calculation, but it is true that without the right
>>> tools,
>>> > you do have a problem. But I realize now that I didn't match my VDW
>>> radii
>>> > with theirs. (I'll reply to Angel in a minute.) Maybe you can check
>>> some of
>>> > this out and get back to us?.
>>> >
>>> > Wed, Sep 2, 2009 at 1:11 PM, N David Brown <[email protected]>
>>> wrote:
>>> >>
>>> >> Given the 677 compounds tested and the proximity to the TSAR values, I
>>> >> think that's an odd comment. It's an approximation, true, but for the
>>> >> drop in computational cost I find the accuracy astounding.
>>> >>
>>> >> Thanks for the isosurface command I requested.
>>> >>
>>> >>
>>> >> 2009/9/2 Robert Hanson <[email protected]>:
>>> >> > So I read that JOC article... I think both their methods are crap.
>>> Jmol
>>> >> > should be doing a much better job because it is the ACTUAL area, not
>>> >> > some
>>> >> > (gross) approximation.
>>> >> >
>>> >> > Bob
>>> >> >
>>> >> >
>>> >> > On Wed, Sep 2, 2009 at 10:58 AM, Robert Hanson <[email protected]>
>>> >> > wrote:
>>> >> >>
>>> >> >> Using Jmol 11.8:
>>> >> >>
>>> >> >> isosurface volume sasurface 0
>>> >> >>
>>> >> >> should do it. You might have to increase the resolution for good
>>> >> >> results:
>>> >> >>
>>> >> >> isosurface resolution 10 volume sasurface 0
>>> >> >>
>>> >> >> keep increasing the number until you are satisfied.
>>> >> >>
>>> >> >> I'll also check that reference. Maybe we can implement that.
>>> >> >>
>>> >> >> Bob
>>> >> >>
>>> >> >>
>>> >> >> On Wed, Sep 2, 2009 at 10:10 AM, N David Brown <
>>> [email protected]>
>>> >> >> wrote:
>>> >> >>>
>>> >> >>> Ok, thanks for the info, Angel :o)
>>> >> >>>
>>> >> >>> Bob, clarification please?
>>> >> >>>
>>> >> >>> I've just found an intriguing paper indeed, "Fast calculation of
>>> van
>>> >> >>> der Waals volume as a sum of atomic bond contributions and its
>>> >> >>> application to drug compounds" by Zhao, Abraham and Zissimos (J.
>>> Org.
>>> >> >>> Chem. 2003, 68, 7368-7373). They describe a method of calculating
>>> the
>>> >> >>> vdW volume using utterly trivial maths - so simple they actually
>>> test
>>> >> >>> it in an Excel spreadsheet! Incredibly it seems to work to a high
>>> >> >>> accuracy; examples they provide show deviation from the MacroModel
>>> >> >>> calc'd value (the long but accurate calculation method) of at most
>>> ~19
>>> >> >>> Angstroms. Very happy they've discovered this!
>>> >> >>>
>>> >> >>> David
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>> 2009/9/2 Angel Herráez <[email protected]>:
>>> >> >>> > David, I remebmer reading of a recent feature in Jmol that
>>> offers
>>> >> >>> > the
>>> >> >>> > volume inside an isosurface. Maybe that can be extended or
>>> matched
>>> >> >>> > to
>>> >> >>> > a vdW surface (there are many options in the isosurface command)
>>> >> >>> >
>>> >> >>> > Surely Bob will tell you, but you can follow that line --and let
>>> us
>>> >> >>> > know :-)
>>> >> >>> >
>>> >> >>> >
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> >> >>>
>>> ------------------------------------------------------------------------------
>>> >> >>> Let Crystal Reports handle the reporting - Free Crystal Reports
>>> 2008
>>> >> >>> 30-Day
>>> >> >>> trial. Simplify your report design, integration and deployment -
>>> and
>>> >> >>> focus on
>>> >> >>> what you do best, core application coding. Discover what's new
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>>> >> >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>>> >> >>> _______________________________________________
>>> >> >>> Jmol-users mailing list
>>> >> >>> [email protected]
>>> >> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >> Robert M. Hanson
>>> >> >> Professor of Chemistry
>>> >> >> St. Olaf College
>>> >> >> 1520 St. Olaf Ave.
>>> >> >> Northfield, MN 55057
>>> >> >> http://www.stolaf.edu/people/hansonr
>>> >> >> phone: 507-786-3107
>>> >> >>
>>> >> >>
>>> >> >> If nature does not answer first what we want,
>>> >> >> it is better to take what answer we get.
>>> >> >>
>>> >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>> >> >
>>> >> >
>>> >> >
>>> >> > --
>>> >> > Robert M. Hanson
>>> >> > Professor of Chemistry
>>> >> > St. Olaf College
>>> >> > 1520 St. Olaf Ave.
>>> >> > Northfield, MN 55057
>>> >> > http://www.stolaf.edu/people/hansonr
>>> >> > phone: 507-786-3107
>>> >> >
>>> >> >
>>> >> > If nature does not answer first what we want,
>>> >> > it is better to take what answer we get.
>>> >> >
>>> >> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>> >> >
>>> >
>>> >
>>> >
>>> > --
>>> > Robert M. Hanson
>>> > Professor of Chemistry
>>> > St. Olaf College
>>> > 1520 St. Olaf Ave.
>>> > Northfield, MN 55057
>>> > http://www.stolaf.edu/people/hansonr
>>> > phone: 507-786-3107
>>> >
>>> >
>>> > If nature does not answer first what we want,
>>> > it is better to take what answer we get.
>>> >
>>> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>> >
>>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Professor of Chemistry
>> St. Olaf College
>> 1520 St. Olaf Ave.
>> Northfield, MN 55057
>> http://www.stolaf.edu/people/hansonr
>> phone: 507-786-3107
>>
>>
>> If nature does not answer first what we want,
>> it is better to take what answer we get.
>>
>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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