From owner-chemistry@ccl.net Thu Aug 11 04:52:01 2011
From: "Gonzalo Jimenez Oses gonzalo.jimenez(a)unirioja.es" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Residue annotation in MOZYME
Message-Id: <-45239-110811044953-25365-rJgIw2zR/3KJ03w7m2ylcQ _ server.ccl.net>
X-Original-From: "Gonzalo  Jimenez Oses" <gonzalo.jimenez**unirioja.es>
Date: Thu, 11 Aug 2011 04:49:50 -0400


Sent to CCL by: "Gonzalo  Jimenez Oses" [gonzalo.jimenez^-^unirioja.es]
Dear all,

I have observed that MOPAC overrides the residue labels specified in the PDB 
files when they are used as inputs for MOZYME. For example, a Pro can be 
automatically changed into a Val after reading the PDB input. This has terrible 
consequences for the global charge computation. Of course, one can fix the 
carge manually, but this is not very convenient when processing dozens of PDB 
files in batch mode.

The cause of these changes is very slight deviations from the "ideal" residue 
geometry (I have overriden this bug by just changing the XYZ coordinates of 
just one atom of the conflictive Pro).
So, my question is: given that the residue labels are already specified in the 
PDB file, is there any way to override the automatic re-tagging of the residues 
before any MOZYME calculation?
I have checked the documentation, but have not found anything.

Thanks a lot, best regards,

Gonzalo


From owner-chemistry@ccl.net Thu Aug 11 06:56:00 2011
From: "sana_gul-x-iccs.edu" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL:G: Regarding Electrostatic potential calculation
Message-Id: <-45240-110811060653-14704-cyn5crIZaOSk0BpA6k/20w!=!server.ccl.net>
X-Original-From: sana_gul_._iccs.edu
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Date: Thu, 11 Aug 2011 15:06:25 +0500
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Sent to CCL by: sana_gul[#]iccs.edu
Hello,

First you have to make file i.e. com (format) either by using openbabel or
g03 and then this filename.com will be used as input to calculate ESP from
g03 and you can use this command
g03 filename.com

Regards



> Dear all,
>              I wanted calculate electrostatic potentials of each atom in a
> molecule using G03. Can anybody send me the keyword for calculating ESP
> using CHelp algorithm in gaussian.
>
>
> Thank you in advance.
>
> With regards,
> Ravi Kumar V.
> IISc
> India.
>


From owner-chemistry@ccl.net Thu Aug 11 07:31:00 2011
From: "Vladimir Chupakhin chupvl[A]gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: models to predict small molecule fluorescence, publications?
Message-Id: <-45241-110810132240-11580-APXAUPT2ISiNCRvfz8GO2A]*[server.ccl.net>
X-Original-From: Vladimir Chupakhin <chupvl-x-gmail.com>
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Date: Wed, 10 Aug 2011 19:22:06 +0200
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Sent to CCL by: Vladimir Chupakhin [chupvl|,|gmail.com]
--000e0cd48ebe90c1ab04aa29ec32
Content-Type: text/plain; charset=UTF-8

Hello,

try to search smthing like bodipy + fluorescence + prediction. But to
my knowledge the fluorescence prediction is quit a task even with QM gives
poor results. Using chemoinformatics (QSPR) you can gain the good models
with similar compounds, but probably will totally fail with external test
sets of noncongeneric compounds.

*Vladimir Chupakhin*,
*Postdoc at joint project between*
*Chemoinformatics laboratory and*
*Structural Chemogenomics group*
*University of Strasbourg, Strasbourg, France*
*
*



On Wed, Aug 10, 2011 at 6:03 PM, James Thomas Metz James.Metz^_^Abbott.com <
owner-chemistry\a/ccl.net> wrote:

>
> Sent to CCL by: "James Thomas Metz" [James.Metz+/-Abbott.com]
> CCL,
>
> Can someone direct me to any publications describing models to predict
> small molecule fluorescence using cheminformatics-type approaches i.e.,
> pattern recognition of aromatic rings or substructures which have a high
> probability
> of fluorescence.
>
> I am trying to avoid QM or semi-empirical approaches, if possible.
>
> Alternatively, if someone is aware of databases of compounds which have
> been
> tested for fluorescence and contain positives and negatives that would be
> excellent.  I have access to software that would allow me to construct
> in-house
> models given enough quality data.
>
> Thank you.
>
> Regards,
> Jim Metz
> Abbott Laboratories>
>
>

--000e0cd48ebe90c1ab04aa29ec32
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<div>Hello,</div><div><br></div><div>try to search smthing like bodipy + fl=
uorescence + prediction. But to my=C2=A0knowledge=C2=A0the=C2=A0fluorescenc=
e prediction is quit a task even with QM gives poor results. Using chemoinf=
ormatics (QSPR) you can gain the good models with similar compounds, but pr=
obably will totally fail with external test sets of noncongeneric compounds=
.</div>

<meta http-equiv=3D"content-type" content=3D"text/html; charset=3Dutf-8"><b=
r clear=3D"all"><b>Vladimir Chupakhin</b>,<div><i>Postdoc at joint project =
between</i></div><div><i>Chemoinformatics laboratory and</i></div><div><i>S=
tructural Chemogenomics group</i></div>

<div><i>University of Strasbourg, Strasbourg, France</i></div><div><i><br><=
/i></div><br>
<br><br><div class=3D"gmail_quote">On Wed, Aug 10, 2011 at 6:03 PM, James T=
homas Metz James.Metz^_^Abbott.com <span dir=3D"ltr">&lt;<a href=3D"mailto:=
owner-chemistry\a/ccl.net">owner-chemistry\a/ccl.net</a>&gt;</span> wrote:<br><=
blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px=
 #ccc solid;padding-left:1ex;">

<br>
Sent to CCL by: &quot;James Thomas Metz&quot; [James.Metz+/-Abbott.com]<br>
CCL,<br>
<br>
Can someone direct me to any publications describing models to predict smal=
l molecule fluorescence using cheminformatics-type approaches i.e., pattern=
 recognition of aromatic rings or substructures which have a high probabili=
ty<br>


of fluorescence.<br>
<br>
I am trying to avoid QM or semi-empirical approaches, if possible.<br>
<br>
Alternatively, if someone is aware of databases of compounds which have bee=
n<br>
tested for fluorescence and contain positives and negatives that would be e=
xcellent. =C2=A0I have access to software that would allow me to construct =
in-house<br>
models given enough quality data.<br>
<br>
Thank you.<br>
<br>
Regards,<br>
Jim Metz<br>
Abbott Laboratories<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
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</blockquote></div><br>

--000e0cd48ebe90c1ab04aa29ec32--


From owner-chemistry@ccl.net Thu Aug 11 13:23:00 2011
From: "Y. Yuan echemistry##yahoo.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Chrawler - Chemistry Crawler for personal computers
Message-Id: <-45242-110811070343-2436-WH7Wy0qVOtcaqKHrypIjew]*[server.ccl.net>
X-Original-From: "Y. Yuan" <echemistry#,#yahoo.com>
Content-Type: multipart/alternative; boundary="0-1720492613-1313060615=:62297"
Date: Thu, 11 Aug 2011 04:03:35 -0700 (PDT)
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Sent to CCL by: "Y. Yuan" [echemistry::yahoo.com]
--0-1720492613-1313060615=:62297
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
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From owner-chemistry@ccl.net Thu Aug 11 14:17:00 2011
From: "Victor Rosas Garcia rosas.victor]_[gmail.com" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: SUMMARY: dft for radicals?
Message-Id: <-45243-110811131054-16584-z+iFeiTVYejnAKsY47p+yA]-[server.ccl.net>
X-Original-From: Victor Rosas Garcia <rosas.victor-*-gmail.com>
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Date: Thu, 11 Aug 2011 12:10:44 -0500
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Sent to CCL by: Victor Rosas Garcia [rosas.victor[A]gmail.com]
Hello everybody,

Well, it's been a week since I posted my question and it lools like no
more replies are coming by.  The original question was:

I'm looking for a functional suitable for radicals (phenoxy type) for
the calculation of bond dissociation energies and spin densities. So
far my library search has not turned up much.  Of course, I have found
a ton of dft studies on radicals, but no review that discusses the
relative merits of different functionals for this kind of calculation.
Can anyone point to a review of this kind?

Thanks to (in no particular order):

William McDonald, for his paper where he shows that "the pbe0
functional with C-PCM solvent predicts very accurate O-H bond
dissociation energies for carefully constructed isodesmic reactions
involving phenoxyl radicals. See J. Phys. Chem. B 2010, 114, 6409–6425
(doi: 10.1021/jp909574v)"

Alcides Simao, for pointing out the paper
Bernardi, Fernando, Andrea Bottoni, and Marco Garavelli. “Exploring
Organic Chemistry with DFT: Radical, Organo‐metallic, and Bio‐organic
Applications.” Quantitative Structure‐Activity Relationships 21, no. 2
(July 1, 2002): 128-148.

Tobias Schwabe, for pointing out the GMTKN30 benchmark set, located at
http://toc.uni-muenster.de/GMTKN/GMTKN30/RSE43.html, indicating that
self-interaction is a serious problem in aromatic radicals and
suggesting double-hybrids for these.

Lars Goerick, for recommending "a look at some of Leo Radoms recent
publications (of the last 2-3 years) on RSEs and BDEs. The
Radom group also comes to the conclusion that double-hybrids work
particularly well for radicals."

All these amounts to A LOT of reading so, I have not decided yet on
what functional to use, but I'm getting there.

Have a nice day!

Victor