From owner-chemistry@ccl.net Fri Aug 24 01:07:00 2007
From: "David Gallagher gallagher.da_+_gmail.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Semi empirical PBC program
Message-Id: <-35006-070823223905-5699-Gv0dSkACF+VUjYZbmvNKmA]*[server.ccl.net>
X-Original-From: David Gallagher <gallagher.da(-)gmail.com>
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Date: Thu, 23 Aug 2007 18:42:13 -0700
Mime-Version: 1.0
Sent to CCL by: David Gallagher [gallagher.da_+_gmail.com]
MOPAC2007 uses 'translation vectors' to do geometry optimizations on
extended solids such as crystals. It is free for academic and
not-for-profit use. There is more information at
http://www.openmopac.net/MOPAC2007.html
Regards
David Gallagher
CAChe Research
At 01:58 PM 8/23/2007, Green Power powergreen%a%gmail.com wrote:
>Dear All,
>
>Can you recommed a free semiempirical PBC program, which can perform
>geometry optimization? Thank you in advance.
>
>Tian
From owner-chemistry@ccl.net Fri Aug 24 05:56:01 2007
From: "Szabolcs Csepregi scsepregi(~)chemaxon.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: fragment-substructure search
Message-Id: <-35007-070824051534-9100-SrDqcA0DjTO4zHRbnOO8ag[A]server.ccl.net>
X-Original-From: Szabolcs Csepregi <scsepregi . chemaxon.com>
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Date: Fri, 24 Aug 2007 11:15:22 +0200
MIME-Version: 1.0
Sent to CCL by: Szabolcs Csepregi [scsepregi*|*chemaxon.com]
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Hi Efrat,<br>
<br>
JChem can do that in many ways:<br>
<br>
1. There is a JChem Oracle Cartridge operator jc_matchcount:<a
href="http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_matchcount"></a><br>
<a class="moz-txt-link-freetext" href="http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_matchcount">http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_matchcount</a><br>
<br>
2. The jcsearch
command-line program can do this also using the "-t:c --allHits"
option:<br>
<br>
$ jcsearch -t:c --allHits -q c1ccccc1 c1ccc2ccccc2c1<br>
2<br>
<br>
See: <a class="moz-txt-link-freetext" href="http://www.chemaxon.com/jchem/doc/user/Jcsearch.html">http://www.chemaxon.com/jchem/doc/user/Jcsearch.html</a><br>
<br>
3. There is a matchCount
function in the Chemical
Terms language for this. This language can be used in many places
at various ChemAxon products, for example you can set up calculated
columns in Instant JChem or JChem Base.<br>
For more information, see:<br>
<span class="moz-txt-link-freetext"><a class="moz-txt-link-freetext" href="http://www.chemaxon.com/instantjchem/ijc_2_0/docs/user/help/htmlfiles/chemical_terms/adding_chem_terms_fields.html">http://www.chemaxon.com/instantjchem/ijc_2_0/docs/user/help/htmlfiles/chemical_terms/adding_chem_terms_fields.html</a></span><br>
<a class="moz-txt-link-freetext" href="http://www.chemaxon.com/chemterms.html">http://www.chemaxon.com/chemterms.html</a><br>
<a class="moz-txt-link-freetext" href="http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchcountdesc">http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchcountdesc</a><br>
<br>
<br>
4. There are also a function in the programming interface:
MolSearch.getMatchCount()<br>
See:<br>
<a class="moz-txt-link-freetext" href="http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/MolSearch.html">http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/MolSearch.html</a><br>
<a class="moz-txt-link-freetext" href="http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/Search.html#getMatchCount%28%29">http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/Search.html#getMatchCount%28%29</a><br>
<a
href="http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/Search.html#getMatchCount%28%29"></a><br>
All of the above understands many file formats and can handle various
query features such as SMARTS, etc.<br>
Probably the most straightforward to use is 3 (Instant JChem), which
happens to be free for local database usage.<br>
<br>
I hope this helps.<br>
Szabolcs
<pre class="moz-signature" cols="72">Szabolcs Csepregi, PhD
Director of Search Technologies, ChemAxon Ltd.
<a class="moz-txt-link-freetext" href="http://www.chemaxon.com">http://www.chemaxon.com</a>
Skype: szabolcs.csepregi
Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659
</pre>
<br>
Efrat Noy enoy%a%epixpharma.com wrote:
<blockquote
cite="mid:-id%234vz-35000-070823112445-8492-DhvkCYMZPYuc+pChcLNVDw:-:server.ccl.net"
type="cite">
<pre wrap="">Sent to CCL by: "Efrat Noy" [enoy++epixpharma.com]
Hi All,
I am looking for a tool capable of counting non-overlapping instances of substructure-fragments in a set of molecules, yet counting partially overlapping fragments. For example, counting two instances of a benzene fragment in a naphtalene molecule.
Are you familiar with any tool able to do that?
Thanks
enoy]_[epixpharma.comE-mail to subscribers: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY:-:ccl.net">CHEMISTRY:-:ccl.net</a> or use:
<a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>
E-mail to administrators: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY-REQUEST:-:ccl.net">CHEMISTRY-REQUEST:-:ccl.net</a> or use
<a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a<a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a>
Before posting, check wait time at: <a class="moz-txt-link-freetext" href="http://www.ccl.net">http://www.ccl.net</a>
Job: <a class="moz-txt-link-freetext" href="http://www.ccl.net/jobs">http://www.ccl.net/jobs</a>
Conferences: <a class="moz-txt-link-freetext" href="http://server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.net/chemistry/announcements/conferences/</a>
Search Messages: <a class="moz-txt-link-freetext" href="http://www.ccl.net/htdig">http://www.ccl.net/htdig</a> (login: ccl, Password: search)<a class="moz-txt-link-freetext" href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a>
RTFI: <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a</pre>
</blockquote>
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From owner-chemistry@ccl.net Fri Aug 24 08:40:00 2007
From: "Selva Kumar K kumarselvak/./gmail.com" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: How to analyse the ADF fragment results
Message-Id: <-35008-070824012725-1127-XhWfgZGmbWKvyOrJiHYGhw],[server.ccl.net>
X-Original-From: "Selva Kumar K" <kumarselvak() gmail.com>
Date: Fri, 24 Aug 2007 01:27:22 -0400
Sent to CCL by: "Selva Kumar K" [kumarselvak()gmail.com]
Hi Dear CCL users
i have problem with separating the values from ADF fragment results of Eint, EPauli, Eelstat,Eorb,Esigma,Epi, Eprep. I run the calculation as in journal chem. Eur. J. 2006, 12, 3617-3629 and got the below results from ADF 2006.01 package for trans-butadiene molecule i want know how to separte out these terms
EDA results of two fragments of trans-butadiene through central single C-C bond
Basis set: TZ2P
Core type: None
Intergration Accuracy:4.0
XC potential in SCF: CGA:BP
hartree eV kcal/mol kJ/mol
-------------------- ----------- ---------- -----------
Pauli Repulsion
Kinetic (Delta T^0): 2.507525218690230 68.2332 1573.50 6583.51
Delta V^Pauli Coulomb: -1.111292107969481 -30.2398 -697.35 -2917.70
Delta V^Pauli LDA-XC: -0.350704427136799 -9.5432 -220.07 -920.77
Delta V^Pauli GGA-Exchange: 0.030335613285599 0.8255 19.04 79.65
Delta V^Pauli GGA-Correlation: -0.009894321200965 -0.2692 -6.21 -25.98
-------------------- ----------- ---------- -----------
Total Pauli Repulsion: 1.065969975668584 29.0065 668.91 2798.70
(Total Pauli Repulsion =
Delta E^Pauli in BB paper)
Steric Interaction
Pauli Repulsion (Delta E^Pauli): 1.065969975668584 29.0065 668.91 2798.70
Electrostatic Interaction: -0.282882130033105 -7.6976 -177.51 -742.71
(Electrostatic Interaction =
Delta V_elstat in the BB paper)
-------------------- ----------- ---------- -----------
Total Steric Interaction: 0.783087845635479 21.3089 491.40 2056.00
(Total Steric Interaction =
Delta E^0 in the BB paper)
Orbital Interactions
AA: -0.994625918381074 -27.0651 -624.14 -2611.39
AAA: -0.030826084764200 -0.8388 -19.34 -80.93
-------------------- ----------- ---------- -----------
Total Orbital Interactions: -1.025452003145274 -27.9040 -643.48 -2692.32
Alternative Decomposition Orb.Int.
Kinetic: -2.113402444942369 -57.5086 -1326.18 -5548.74
Coulomb: 1.000503276660340 27.2251 627.83 2626.82
XC: 0.087447165136791 2.3796 54.87 229.59
-------------------- ----------- ---------- -----------
Total Orbital Interactions: -1.025452003145238 -27.9040 -643.48 -2692.32
Residu (E=Steric+OrbInt+Res): -0.000000308266483 0.0000 0.00 0.00
Total Bonding Energy: -0.242364465776277 -6.5951 -152.09 -636.33
Summary of Bonding Energy (energy terms are taken from the energy decomposition above)
======================================================================================
Electrostatic Energy: -0.282882130033105 -7.6976 -177.51 -742.71
Kinetic Energy: 0.394122773747861 10.7246 247.32 1034.77
Coulomb (Steric+OrbInt) Energy: -0.110789139575624 -3.0147 -69.52 -290.88
XC Energy: -0.242815969915374 -6.6074 -152.37 -637.51
-------------------- ----------- ---------- -----------
Total Bonding Energy: -0.242364465776241 -6.5951 -152.09 -636.33
---------------------------------------------------------------------------------------------------------
In Chem. Eur. J. 2006, 12, 3617-3629 Conjugation and Hyperconjugation Full Paper reported in page 3619
trans-butadiene all values in Kcal/mol
Eint -128.5
EPauli 268.4
Eelstat -169.9
Eorb -227.5
Esigma -207.5
Epi -19.5
Eprep 13.0
please help me out how to calculate all this values from the above ADF results
thanks in advance
Selva KK
From owner-chemistry@ccl.net Fri Aug 24 09:11:01 2007
From: "Yangsoo Kim vsmember::gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL:G: Thermochemical calculations from Gaussian output file
Message-Id: <-35009-070824012444-32474-YWhLm4nzs4gos34oDW1vDQ : server.ccl.net>
X-Original-From: "Yangsoo Kim" <vsmember(-)gmail.com>
Date: Fri, 24 Aug 2007 01:24:40 -0400
Sent to CCL by: "Yangsoo Kim" [vsmember-x-gmail.com]
Dear all,
Im wondering if anyone of you performed the thermochemical calculations from Gaussian output. What wed like to do is to calculate heat of formation, ionization energy, electron affinity, proton affinity, and bond dissociation energy from Gaussian output files.
We first tried to perform those calculations based on some published approaches (e.g., Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds, L. A. Curtiss, P. C. Redfern, and D. J. Frurip, Reviews of Computational Chemistry, Volume 15 Edited by K. B. Lipkowitz and D. B. Boyd pp.147-202). Unfortunately, our calculation results do not match the data that have been available in the computational thermochemistry literature.
I'd appreciate if anyone can suggest how to get those thermochmical property values out of Gaussian output file. Due to our tight project schedule, it would be the best if any commercial or open (free) code or software is available.
Any comments on this matter would be greatly appreciated, and I'll summarize the replies.
Thanks in advance,
Yangsoo Kim, Ph.D.
From owner-chemistry@ccl.net Fri Aug 24 09:50:00 2007
From: "Rajarshi Guha rguha- -indiana.edu" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Open Source 3D coordinate generation tool
Message-Id: <-35010-070824061302-19664-Yn2ul88nuJd1q4m2zSe40g * server.ccl.net>
X-Original-From: Rajarshi Guha <rguha-,-indiana.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
Date: Fri, 24 Aug 2007 06:12:55 -0400
Mime-Version: 1.0 (Apple Message framework v752.3)
Sent to CCL by: Rajarshi Guha [rguha-.-indiana.edu]
On Aug 22, 2007, at 12:00 PM, Lothar Terfloth lothar.terfloth|,|
chemie.uni-erlangen.de wrote:
>
> Sent to CCL by: Lothar Terfloth [lothar.terfloth,chemie.uni-
> erlangen.de]
>
> Dear all,
>
> a) SPE is the central step for the generation of a 'rough' set of
> 3D coordinates in smi23d.
> Following
>
> http://www.wipo.int/pctdb/en/wo.jsp?
> wo=2004003683&IA=WO2004003683&DISPLAY=STATUS
>
> or
>
> http://www.wipo.int/pctdb/en/wo.jsp?
> wo=2004003683&IA=WO2004003683&DISPLAY=STATUS
>
> I would assume that there is a patent on the SPE algorithm and its
> application. Does this affect smi23d?
I will get more concrete information regarding this in a few days
>
> b) Obviously smi2sdf does not support stereochemistry, e.g.
>
> butene.smi:
> C\C=C\C E-but-2-ene
> C\C=C/C Z-but-2-ene
smi2sdf does support E/Z stereochemistry and this was a bug - the
latest fixed version is in SVN and builds for OS X and Linux (Fedora
Core 64 bit) have been updated
> I tried also cis- and trans-decalin.
>
> decalin.smi:
> [H][C*o**o*]12[C*o**o*](CCCC2)([H])CCCC1 cis-decalin
> [H][C*o**o*]12[C*o*](CCCC2)([H])CCCC1 trans-decalin
I'm not aware of the use of the '*' token to indicate tetrahedral
chirality. If on the other hand I use the following:
C1CC[C * * H]2CCCC[C * H]2C1 trans-decalin
C1CC[C * H]2CCCC[C * H]2C1 cis-decalin
it works fine
> c) I made a very brief comparision with CORINA on a data set
> of 146 cytochrome P450 substrates which has been published
> recently (http://dx.doi.org/10.1021/ci700010t & suppl. material).
Thanks for the comparison - we certainly make no claims to speed :)
We are in the process of generating benchmarks wrt timing and ability
to handle complex molecules.
> d) How long did it take to generate Pub3D?
This is a little tricky to answer since we switched between different
machines as well as had to regenerate certain portions of the
database while we got our workflow in place. Overall we took about a
month or so, but this is obviously not a rigorous statement since
there was a number of days of downtime etc.
As I noted above, we'll be running benchmarks so hopefully in the
next few weeks we'll get a more rigorous answer
> e) Is mengine based on Pcmodel version 7? ( http://
> www.serenasoft.com )
As with a), I'll get back to you in a few days
-------------------------------------------------------------------
Rajarshi Guha <rguha * indiana.edu>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
A mathematician is a device for turning coffee into theorems.
-- P. Erdos
From owner-chemistry@ccl.net Fri Aug 24 10:20:01 2007
From: "Yangsoo Kim vsmember++gmail.com" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL:G: CCL Thermochemical calculations from Gaussian output file
Message-Id: <-35011-070824013155-3076-bJZEeHvWsU8tt9iyTYOO7g[]server.ccl.net>
X-Original-From: "Yangsoo Kim" <vsmember~~gmail.com>
Date: Fri, 24 Aug 2007 01:31:52 -0400
Sent to CCL by: "Yangsoo Kim" [vsmember%x%gmail.com]
Dear all,
Im wondering if anyone of you performed the thermochemical calculations from Gaussian output. What wed like to do is to calculate heat of formation, ionization energy, electron affinity, proton affinity, and bond dissociation energy from Gaussian output files.
We first tried to perform those calculations based on some published approaches (e.g., Theoretical Methods for Computing Enthalpies of Formation of Gaseous Compounds, L. A. Curtiss, P. C. Redfern, and D. J. Frurip, Reviews of Computational Chemistry, Volume 15 Edited by K. B. Lipkowitz and D. B. Boyd pp.147-202). Unfortunately, our calculation results do not match the data that have been available in the computational thermochemistry literature.
I'd appreciate if anyone can suggest how to get those thermochmical property values out of Gaussian output file. Due to our tight project schedule, it would be the best if any commercial or open (free) code or software is available.
Any comments on this matter would be greatly appreciated, and I'll summarize the replies.
Thanks in advance,
Yangsoo Kim, Ph.D.
From owner-chemistry@ccl.net Fri Aug 24 10:55:01 2007
From: "Yun Wang wangyun22%yahoo.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Semi empirical PBC program
Message-Id: <-35012-070823212438-29749-tZcOuntb3vVg6RwthIMQog__server.ccl.net>
X-Original-From: Yun Wang <wangyun22^^yahoo.com>
Content-Type: multipart/alternative; boundary="0-607431699-1187915072=:18689"
Date: Thu, 23 Aug 2007 17:24:32 -0700 (PDT)
MIME-Version: 1.0
Sent to CCL by: Yun Wang [wangyun22.:.yahoo.com]
--0-607431699-1187915072=:18689
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable
MOPAC 7=0A=0A=0A----- Original Message ----=0AFrom: Green Power powergreen%=
a%gmail.com <owner-chemistry:_:ccl.net>=0ATo: "Wang, Yun " <wangyun22=
:_:yahoo.com>=0ASent: Friday, 24 August, 2007 6:58:26 AM=0ASubject: CCL: Semi=
empirical PBC program=0A=0A=0ADear All,=0A =0ACan you recommed a free semi=
empirical PBC program, which can perform geometry optimization? Thank you i=
n advance.=0A =0ATian=0A=0A=0A _______________________________________=
_____________________________________________=0ASick of deleting your inbox=
? Yahoo!7 Mail has free unlimited storage.=0Ahttp://au.docs.yahoo.com/mail/=
unlimitedstorage.html=0A
--0-607431699-1187915072=:18689
Content-Type: text/html; charset=iso-8859-1
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<html><head><style type=3D"text/css"><!-- DIV {margin:0px;} --></style></he=
ad><body><div style=3D"font-family:times new roman, new york, times, serif;=
font-size:12pt"><DIV style=3D"FONT-SIZE: 12pt; FONT-FAMILY: times new roman=
, new york, times, serif">MOPAC 7<BR><BR>=0A<DIV style=3D"FONT-SIZE: 12pt; =
FONT-FAMILY: times new roman, new york, times, serif">----- Original Messag=
e ----<BR>From: Green Power powergreen%a%gmail.com <owner-chemistry:_:ccl.=
net><BR>To: "Wang, Yun " <wangyun22:_:yahoo.com><BR>Sent: Fr=
iday, 24 August, 2007 6:58:26 AM<BR>Subject: CCL: Semi empirical PBC progra=
m<BR><BR>=0A<DIV>Dear All,</DIV>=0A<DIV> </DIV>=0A<DIV>Can you recomme=
d a free semiempirical PBC program, which can perform geometry optimization=
? Thank you in advance.</DIV>=0A<DIV> </DIV>=0A<DIV>Tian </DIV></=
DIV><BR></DIV></div><br>=0A <hr size=3D1>=0ASick of deleting your inbo=
x? Yahoo!7 Mail has free unlimited storage. <a href=3D"http://au.rd.yahoo.c=
om/mail/taglines/optusnet/storage/*http://au.docs.yahoo.com/mail/unlimiteds=
torage.html" target=3D_blank>Get it now</a>.=0A</body></html>
--0-607431699-1187915072=:18689--
From owner-chemistry@ccl.net Fri Aug 24 11:29:01 2007
From: "Close, David M. CLOSED{=}mail.etsu.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: Thermochemical calculations from Gaussian output file
Message-Id: <-35013-070824100835-17936-bUOleSw15kDJCSW3uHyDEA[A]server.ccl.net>
X-Original-From: "Close, David M." <CLOSED{}mail.etsu.edu>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
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charset="us-ascii"
Date: Fri, 24 Aug 2007 10:08:27 -0400
MIME-Version: 1.0
Sent to CCL by: "Close, David M." [CLOSED,mail.etsu.edu]
Yangsoo:
For the thermodynamic information you must run a FREQ calculation from
the normal Gaussian output (from the .chk file). This is describe in
the Gaussian Manual. For ionization energy you have to calculate the
difference in energy between the ground state and the one electron
oxidized state. This involves a separate calculation on the cation. For
the electron affinity, you also have to do a separate calculation. Here
I would suggest a thorough literature search. Depending on the system
you are studying, there a many problems deciding on what bases set and
method to use to get reliable electron affinities.
Regards, Dave Close.
From owner-chemistry@ccl.net Fri Aug 24 12:05:01 2007
From: "Lothar Terfloth lothar.terfloth(~)chemie.uni-erlangen.de" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Open Source 3D coordinate generation tool
Message-Id: <-35014-070824105529-20444-mIEgMjoUoCy79UMqIYzFdw]*[server.ccl.net>
X-Original-From: Lothar Terfloth <lothar.terfloth]|[chemie.uni-erlangen.de>
Content-Transfer-Encoding: 7bit
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Date: Fri, 24 Aug 2007 16:55:19 +0200
MIME-Version: 1.0
Sent to CCL by: Lothar Terfloth [lothar.terfloth\a/chemie.uni-erlangen.de]
Dear Rajarshi Guha,
thanks for your reply.
Concerning tetrahedral chirality it is the notation using the at-sign.
The at-character obviously has been changed automagically by the scripts
processing the e-mails sent to CCL.
The notation using the at-character is briefly explained at
http://www.daylight.com/dayhtml_tutorials/languages/smiles/index.html#STEREO
With best regards,
Lothar Terfloth
Rajarshi Guha rguha- -indiana.edu wrote:
>
> Sent to CCL by: Rajarshi Guha [rguha-.-indiana.edu]
>
> On Aug 22, 2007, at 12:00 PM, Lothar Terfloth
> lothar.terfloth|,|chemie.uni-erlangen.de wrote:
>
>>
>> Sent to CCL by: Lothar Terfloth [lothar.terfloth,chemie.uni-erlangen.de]
>>
>> Dear all,
>>
>> a) SPE is the central step for the generation of a 'rough' set of 3D
>> coordinates in smi23d.
>> Following
>>
>> http://www.wipo.int/pctdb/en/wo.jsp?wo=2004003683&IA=WO2004003683&DISPLAY=STATUS
>>
>>
>> or
>>
>> http://www.wipo.int/pctdb/en/wo.jsp?wo=2004003683&IA=WO2004003683&DISPLAY=STATUS
>>
>>
>> I would assume that there is a patent on the SPE algorithm and its
>> application. Does this affect smi23d?
>
> I will get more concrete information regarding this in a few days
>
>>
>> b) Obviously smi2sdf does not support stereochemistry, e.g.
>>
>> butene.smi:
>> C\C=C\C E-but-2-ene
>> C\C=C/C Z-but-2-ene
>
> smi2sdf does support E/Z stereochemistry and this was a bug - the latest
> fixed version is in SVN and builds for OS X and Linux (Fedora Core 64
> bit) have been updated
>
>> I tried also cis- and trans-decalin.
>>
>> decalin.smi:
>> [H][C*o**o*]12[C*o**o*](CCCC2)([H])CCCC1 cis-decalin
>> [H][C*o**o*]12[C*o*](CCCC2)([H])CCCC1 trans-decalin
>
> I'm not aware of the use of the '*' token to indicate tetrahedral
> chirality. If on the other hand I use the following:
>
> C1CC[C:-::-:H]2CCCC[C:-:H]2C1 trans-decalin
> C1CC[C:-:H]2CCCC[C:-:H]2C1 cis-decalin
>
> it works fine
>
>> c) I made a very brief comparision with CORINA on a data set
>> of 146 cytochrome P450 substrates which has been published
>> recently (http://dx.doi.org/10.1021/ci700010t & suppl. material).
>
> Thanks for the comparison - we certainly make no claims to speed :)
>
> We are in the process of generating benchmarks wrt timing and ability to
> handle complex molecules.
>
>> d) How long did it take to generate Pub3D?
>
> This is a little tricky to answer since we switched between different
> machines as well as had to regenerate certain portions of the database
> while we got our workflow in place. Overall we took about a month or so,
> but this is obviously not a rigorous statement since there was a number
> of days of downtime etc.
>
> As I noted above, we'll be running benchmarks so hopefully in the next
> few weeks we'll get a more rigorous answer
>
>> e) Is mengine based on Pcmodel version 7? ( http://www.serenasoft.com )
>
> As with a), I'll get back to you in a few days
>
> -------------------------------------------------------------------
> Rajarshi Guha <rguha:-:indiana.edu>
> GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
> -------------------------------------------------------------------
> A mathematician is a device for turning coffee into theorems.
> -- P. Erdoshttp://www.ccl.net/chemistry/sub_unsub.shtml>
> Job: http://www.ccl.net/jobsConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
From owner-chemistry@ccl.net Fri Aug 24 12:41:01 2007
From: "Joseph M Leonard jleonard42{:}gmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: GRID questions
Message-Id: <-35015-070824123650-1224-jlxpyt9Y/CgpJL3xeq66Pw*server.ccl.net>
X-Original-From: "Joseph M Leonard" <jleonard42]^[gmail.com>
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boundary="----=_Part_162530_16863145.1187971885719"
Date: Fri, 24 Aug 2007 12:11:25 -0400
MIME-Version: 1.0
Sent to CCL by: "Joseph M Leonard" [jleonard42\a/gmail.com]
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Folks, it's been a while but I've been rereading the GRID source literature,
and I have a few questions I hope CCL readers might know:
1. Is there a published definition of the DRY probe? I recall hearing about
this years ago at a conference, but can't remember when. The best I've
found so far is a short reference in Curr Med Chem 13,2653(2006), which
describes the probe in a sentence or two.
2. Goodford's J Med Chem 28,849(1985) describes the energy functions in
terms of older references (which is not unexpected). However, one of them
is a book by Hopfinger, published in '73... Does anybody have either the
section that describes how the L-J A and B terms are determined, or a copy
of the terms corresponding to this paper?
3. Also in JMC 28 is a mention of K in equation 3. I think this comes from
the CHARMM reference cited (#11), and I'm pursuing that. If anybody has
this on-line I'd appreciate learning its value...
Thanks in advance! I worry that Google's effort in scanning books will take
a while to get to "old chemical literature" :-).
Joe
jleonard42++gmail.com
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Folks, it's been a while but I've been rereading the GRID source literature, and I have a few questions I hope CCL readers might know:<br><br>1. Is there a published definition of the DRY probe? I recall hearing about this years ago at a conference, but can't remember when. The best I've found so far is a short reference in Curr Med Chem 13,2653(2006), which describes the probe in a sentence or two.
<br><br>2. Goodford's J Med Chem 28,849(1985) describes the energy functions in terms of older references (which is not unexpected). However, one of them is a book by Hopfinger, published in '73... Does anybody have either the section that describes how the L-J A and B terms are determined, or a copy of the terms corresponding to this paper?
<br><br>3. Also in JMC 28 is a mention of K in equation 3. I think this comes from the CHARMM reference cited (#11), and I'm pursuing that. If anybody has this on-line I'd appreciate learning its value...<br><br>
Thanks in advance! I worry that Google's effort in scanning books will take a while to get to "old chemical literature" :-).<br><br>Joe<br><a href="mailto:jleonard42++gmail.com">jleonard42++gmail.com</a><br>
------=_Part_162530_16863145.1187971885719--
From owner-chemistry@ccl.net Fri Aug 24 13:49:01 2007
From: "Debellis Anthony CE US anthony.debellis^_^cibasc.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Thermochemical calculations from Gaussian output file
Message-Id: <-35016-070824134427-9583-qg7wiMGDx65Y0TFj817OWw^server.ccl.net>
X-Original-From: "Debellis Anthony CE US" <anthony.debellis[A]cibasc.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
charset="us-ascii"
Date: Fri, 24 Aug 2007 11:24:30 -0400
MIME-Version: 1.0
Sent to CCL by: "Debellis Anthony CE US" [anthony.debellis|cibasc.com]
You might want to have a look at the white paper from Gaussian, Inc.
entitled "Thermochemistry in Gaussian". I'm sure it's available on
their website.
Anthony DeBellis
Ciba
-----Original Message-----
> From: owner-chemistry^-^ccl.net [mailto:owner-chemistry^-^ccl.net]
Sent: Friday, August 24, 2007 1:25 AM
To: Debellis Anthony CE US
Subject: CCL:G: Thermochemical calculations from Gaussian output file
Sent to CCL by: "Yangsoo Kim" [vsmember-x-gmail.com] Dear all,
Im wondering if anyone of you performed the thermochemical calculations
> from Gaussian output. What wed like to do is to calculate heat of
formation, ionization energy, electron affinity, proton affinity, and
bond dissociation energy from Gaussian output files.
We first tried to perform those calculations based on some published
approaches (e.g., Theoretical Methods for Computing Enthalpies of
Formation of Gaseous Compounds, L. A. Curtiss, P. C. Redfern, and D. J.
Frurip, Reviews of Computational Chemistry, Volume 15 Edited by K. B.
Lipkowitz and D. B. Boyd pp.147-202). Unfortunately, our calculation
results do not match the data that have been available in the
computational thermochemistry literature.
I'd appreciate if anyone can suggest how to get those thermochmical
property values out of Gaussian output file. Due to our tight project
schedule, it would be the best if any commercial or open (free) code or
software is available.
Any comments on this matter would be greatly appreciated, and I'll
summarize the replies.
Thanks in advance,
Yangsoo Kim, Ph.D.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt
From owner-chemistry@ccl.net Fri Aug 24 14:26:01 2007
From: "Indranil Rudra indranil.rudra+*+chemistry.gatech.edu" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL:G: C60 atomic coordinates with D3d symmetry
Message-Id: <-35017-070824111403-4666-8gKjdetHRhF7uLUNniHBXA _ server.ccl.net>
X-Original-From: "Indranil Rudra" <indranil.rudra%%chemistry.gatech.edu>
Date: Fri, 24 Aug 2007 11:13:59 -0400
Sent to CCL by: "Indranil Rudra" [indranil.rudra{:}chemistry.gatech.edu]
Dear colleagues,
I was trying to obtain the atomic coordinates of C60 in D3d symmetry. I found from previous ccl mailing list the coordinates for D5d symmetry in gaussian z-matrix format but could not find for D3d symmetry. I was wondering if anyone could help me with the information ?
Regards,
Indranil Rudra
Department of Chemistry and Biochemistry
Georgia Institute of Technology
Atlanta,GA
From owner-chemistry@ccl.net Fri Aug 24 14:59:01 2007
From: "Andrew Orry andy-*-molsoft.com" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: MolSoft ICM Workshop - Protein Structure and Drug Discovery - September 2007
Message-Id: <-35018-070824060311-15643-8q9ITy1fTy7pnOdSkMNtgg=server.ccl.net>
X-Original-From: Andrew Orry <andy%molsoft.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=windows-1252; format=flowed
Date: Thu, 23 Aug 2007 09:49:03 -0700
MIME-Version: 1.0
Sent to CCL by: Andrew Orry [andy-,-molsoft.com]
Molsoft LLC (www.molsoft.com) would like to invite you to an ICM
Workshop entitled "Protein Structure and Drug Discovery" to be held on
September 20th � 21st 2007 in La Jolla, CA, USA. The workshop is
suitable for chemists and biologists who would like to learn more about
computational drug discovery and bioinformatics. No prior knowledge in
this field is required to participate in this workshop. The workshop is
presented by Prof. Ruben Abagyan (Scripps) and Dr. Maxim Totrov (MolSoft).
This workshop consists of lectures, demonstrations and �hands-on�
computational experiments and will cover:
- Sequence and Protein Structure Analysis
- Protein Modeling and Simulations
- Structure Validation and Optimization
- Ligand Binding Site Prediction
- Small Molecule Docking and Virtual Ligand Screening
- Structure-based development of target-specific compound libraries
- Cheminformatics, chemical clustering, searching, superposition ...
- QSAR, machine learning
- Protein-Protein Docking
See www.molsoft.com/training.html for more information.
�The objective of this training workshop is to help chemists and
biologists solve challenging problems in the area of drug discovery by
efficient use of the science and technology present in ICM molecular
modeling tools.� Prof. Ruben Abagyan (The Scripps Research Institute and
Co-Founder of Molsoft LLC)
Please see our website at www.molsoft.com for more details or E mail
andy^molsoft.com or call (858)625 2000 ext.108. MolSoft is a La Jolla
based company that is a primary source of new breakthrough technologies
in computational chemistry and biology. Molsoft is committed to solving
intellectually challenging problems in drug discovery and computational
biology.
From owner-chemistry@ccl.net Fri Aug 24 15:34:00 2007
From: "Shobe, David David.Shobe.]|[.sud-chemie.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL:G: CCL Thermochemical calculations from Gaussian output file
Message-Id: <-35019-070824141451-24081-KJOdXVkl4zqCQ5ozch2dxg]|[server.ccl.net>
X-Original-From: "Shobe, David" <David.Shobe()sud-chemie.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
charset="us-ascii"
Date: Fri, 24 Aug 2007 20:14:37 +0200
MIME-Version: 1.0
Sent to CCL by: "Shobe, David" [David.Shobe^^sud-chemie.com]
Yangsoo,
You won't get an exact match to experimental values, if that's what's
giving you concern. But you should be *close* to the experimental
values if your calculations are good. Even when comparing theoretical
to theoretical heats of formations calc'd at the same level of theory,
you can get different answers depending on which reactions you use and
which values for the "known" heats of formation (such as atomization
energies or reference species like H2O(g) or CH4(g)) you use.
The CBS* and G* methods (G2, G3, and their variants) are the easiest to
use, since they do all the adding and most of the subtracting for you.
Regards,
--David Shobe
-----Original Message-----
> From: owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net]
Sent: Friday, August 24, 2007 1:32 AM
To: Shobe, David
Subject: CCL:G: CCL Thermochemical calculations from Gaussian output
file
Sent to CCL by: "Yangsoo Kim" [vsmember%x%gmail.com]
Dear all,
Im wondering if anyone of you performed the thermochemical calculations
> from Gaussian output. What wed like to do is to calculate heat of
formation, ionization energy, electron affinity, proton affinity, and
bond dissociation energy from Gaussian output files.
We first tried to perform those calculations based on some published
approaches (e.g., Theoretical Methods for Computing Enthalpies of
Formation of Gaseous Compounds, L. A. Curtiss, P. C. Redfern, and D. J.
Frurip, Reviews of Computational Chemistry, Volume 15 Edited by K. B.
Lipkowitz and D. B. Boyd pp.147-202). Unfortunately, our calculation
results do not match the data that have been available in the
computational thermochemistry literature.
I'd appreciate if anyone can suggest how to get those thermochmical
property values out of Gaussian output file. Due to our tight project
schedule, it would be the best if any commercial or open (free) code or
software is available.
Any comments on this matter would be greatly appreciated, and I'll
summarize the replies.
Thanks in advance,
Yangsoo Kim, Ph.D.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message.
Thank you.
From owner-chemistry@ccl.net Fri Aug 24 16:36:01 2007
From: "Michel Petitjean ptitjean[*]itodys.jussieu.fr" <owner-chemistry|*|server.ccl.net>
To: CCL
Subject: CCL: Mol. modeling freewares / Sun computers
Message-Id: <-35020-070824150114-22557-g/hHM0zXYbU0/cDjQSbwcA|*|server.ccl.net>
X-Original-From: Michel Petitjean <ptitjean^^^itodys.jussieu.fr>
Date: Fri, 24 Aug 2007 21:01:03 +0200 (MEST)
Sent to CCL by: Michel Petitjean [ptitjean#%#itodys.jussieu.fr]
To: chemistry .. ccl.net
Subj: Mol. modeling freewares / Sun computers
Hi CCLers,
I have generated versions of my freewares for Sun computers
(binaries are available for both sparc and x64 architectures).
Goto:
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
ARMS: Spatial Alignment with the RMS (Root Mean Square) method.
(needs a pairwise correspondence)
ASV: Analytical calculation of van der Waals surfaces and volumes.
CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules.
(no need of a pairwise correspondence: it is computed)
DOG: Docking Geometrically two molecules.
(needs a pairwise correspondence)
POP: Optimal Partition (classification)
QCM: Quantitative Chirality Measure of a conformer
(graph automorphisms enumeration included)
RADI: Computation of the Radius and Diameter of a spatial set
(plus some other quantities)
Please contact me for any question regarding these products.
I thank the Sun company for providing adequate resources and
I thank the ezqual/isv support team for technical assistance.
Michel Petitjean, Email: petitjean .. itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)
1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57
75005 Paris, France. FAX : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html
From owner-chemistry@ccl.net Fri Aug 24 17:11:01 2007
From: "Karol Langner karol.langner]^[kn.pl" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Thermochemical calculations from Gaussian output file
Message-Id: <-35021-070824162157-28302-dptICmaajcF4SbQRZJHVMA++server.ccl.net>
X-Original-From: Karol Langner <karol.langner_+_kn.pl>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset="iso-8859-1"
Date: Fri, 24 Aug 2007 21:16:22 -0400
MIME-Version: 1.0
Sent to CCL by: Karol Langner [karol.langner,+,kn.pl]
On Friday 24 August 2007 11:24, Debellis Anthony CE US
anthony.debellis^_^cibasc.com wrote:
> Sent to CCL by: "Debellis Anthony CE US" [anthony.debellis|cibasc.com]
> You might want to have a look at the white paper from Gaussian, Inc.
> entitled "Thermochemistry in Gaussian". I'm sure it's available on
> their website.
>
> Anthony DeBellis
> Ciba
Here is the link:
http://www.gaussian.com/g_whitepap/thermo.htm
--
written by Karol Langner
Fri Aug 24 21:16:01 EDT 2007
From owner-chemistry@ccl.net Fri Aug 24 17:47:01 2007
From: "Thomas Heine thomas.heine[A]chemie.tu-dresden.de" <owner-chemistry[#]server.ccl.net>
To: CCL
Subject: CCL:G: C60 atomic coordinates with D3d symmetry
Message-Id: <-35022-070824163842-11092-fs3ipYqnN9UkmsREV0phLg[#]server.ccl.net>
X-Original-From: "Thomas Heine" <thomas.heine^chemie.tu-dresden.de>
Content-Disposition: inline
Content-Transfer-Encoding: 7bit
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Date: Fri, 24 Aug 2007 21:35:59 +0200
MIME-Version: 1.0
Sent to CCL by: "Thomas Heine" [thomas.heine{}chemie.tu-dresden.de]
Try Cage (http://www.math.uni-bielefeld.de/~CaGe/) to create
coordinates but note that there is only one IPR for C60, and that is
Ih.
Regards, Thomas
2007/8/24, Indranil Rudra indranil.rudra+*+chemistry.gaech.edu
<owner-chemistry!A!ccl.net>:
>
> Sent to CCL by: "Indranil Rudra" [indranil.rudra{:}chemistry.gatech.edu]
> Dear colleagues,
> I was trying to obtain the atomic coordinates of C60 in D3d symmetry. I found from previous ccl mailing list the coordinates for D5d symmetry in gaussian z-matrix format but could not find for D3d symmetry. I was wondering if anyone could help me with the information ?
>
> Regards,
> Indranil Rudra
> Department of Chemistry and Biochemistry
> Georgia Institute of Technology
> Atlanta,GA>
>
>
>
From owner-chemistry@ccl.net Fri Aug 24 19:26:01 2007
From: "Jimmy Lawrence jlawrence%x%slb.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL:G: MFI, zeolite structure with Gaussian03
Message-Id: <-35023-070824192527-11743-MlJUHAopw/DOkg6TREUnHQ|a|server.ccl.net>
X-Original-From: Jimmy Lawrence <jlawrence,slb.com>
Content-transfer-encoding: 7BIT
Content-type: text/plain; charset=ISO-8859-1; format=flowed
Date: Fri, 24 Aug 2007 18:25:22 -0400
MIME-version: 1.0
Sent to CCL by: Jimmy Lawrence [jlawrence{:}slb.com]
Hi CCL members,
I am a beginner in calculating this type of system.
Can somebody point a tutorial or share some experience by simple
instruction on how to build the structure of MFI (or other zeolite) with
PBC in Gaussian03 (via GaussView) and how to dock the molecule to
evaluate (e.g. CO2) ?
Thank you,
Jimmy