From owner-chemistry@ccl.net Fri Mar 14 08:11:01 2008
From: "David Close closed##etsu.edu" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL:G: BABEL, Z-matrix, modredundant?
Message-Id: <-36498-080314080917-5929-CmF2jIwuX2bb64/HLKUT0Q.:.server.ccl.net>
X-Original-From: "David Close" <closed]~[etsu.edu>
Date: Fri, 14 Mar 2008 08:09:13 -0400
Sent to CCL by: "David Close" [closed]^[etsu.edu]
I've just installed the new version of BABEL, and have noted that I can't get a z-matrix from the sleected outputs. My old version (DOS) was able to convert crysallographic coordinates directly into Gaussian z-matrix output.
I have always used the z-matrix input to Gaussian jobs when I wanted to freeze some coordinates. But last week there was a discussion on this list on whether or not it is necessary to use a z-matrix if one wants to freeze coordinates using modredundant. I can't seem to find the response to this question.
So my question is, if I can't make BABEL convert an output to a z-matrix,
can I use the normal xyz coordinates and freeze a torsion angle with the Modredundant command?
Regards, Dave Close.
From owner-chemistry@ccl.net Fri Mar 14 09:02:00 2008
From: "Matthew Thompson matthew.thompson.:.nrl.navy.mil" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Elegantly Describing Molecules with a Certain Geometric Property
Message-Id: <-36499-080314082457-13174-BwX1C9/Q7Yy+pDG1r51yYA*server.ccl.net>
X-Original-From: Matthew Thompson <matthew.thompson*|*nrl.navy.mil>
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Sent to CCL by: Matthew Thompson [matthew.thompson#nrl.navy.mil]
Folks, I'm hoping there is a group theory savant or someone on this list
who can help me with a puzzle of mine. Namely, I'm trying to figure out
the best or most concise way to describe a set of molecules, maybe, if
possible, in group theoretical terms.
The set I'm looking at is the set of all uni- and di-elemental molecules
that have *one* representative bond length. Obvious examples are all XY
and all X2 molecules; likewise, H2O, CH4, and SF6 also have one
characteristic bond length.
Thus, I've been wondering if there was some way to describe these
molecules in a concise way with group theory. I can't say all Cnv and
Dnh work since N2O kills that (needs rNN and rNO to describe). I can't
say their point group must be Abelian because of Td and Oh (CH4 and SF6).
I think you could couch it in Z-matrix terms by saying you only need one
distance no matter the length of the Z-matrix (i.e., only one number in
the third column), but that seems sort of inelegant. It seems like
there must be some way to do this but I just can't figure it out. So, I
thought I'd ask CCL and probably get an answer in an instant.
Thanks for any help,
Matt
--
Matt Thompson, PhD
Naval Research Laboratory
202-767-2160
From owner-chemistry@ccl.net Fri Mar 14 10:18:01 2008
From: "Reinaldo Pis Diez reinaldo.pisdiez-.-gmail.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL:G: BABEL, Z-matrix, modredundant?
Message-Id: <-36500-080314095150-31068-ohYAECAtfznXIuhX6BOBhw##server.ccl.net>
X-Original-From: "Reinaldo Pis Diez" <reinaldo.pisdiez%gmail.com>
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Date: Fri, 14 Mar 2008 10:44:54 -0300
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Sent to CCL by: "Reinaldo Pis Diez" [reinaldo.pisdiez|gmail.com]
Dave,
Try the Fenske-Hall z-matrix option for the output format (it is
abbreviated fh). The resulting z-matrix is identical to the one used
in gaussian.
Regards,
Reinaldo
2008/3/14, David Close closed##etsu.edu <owner-chemistry%%ccl.net>:
>
> Sent to CCL by: "David Close" [closed]^[etsu.edu]
> I've just installed the new version of BABEL, and have noted that I can't get a z-matrix from the sleected outputs. My old version (DOS) was able to convert crysallographic coordinates directly into Gaussian z-matrix output.
> I have always used the z-matrix input to Gaussian jobs when I wanted to freeze some coordinates. But last week there was a discussion on this list on whether or not it is necessary to use a z-matrix if one wants to freeze coordinates using modredundant. I can't seem to find the response to this question.
> So my question is, if I can't make BABEL convert an output to a z-matrix,
> can I use the normal xyz coordinates and freeze a torsion angle with the Modredundant command?
> Regards, Dave Close.>
>
>
From owner-chemistry@ccl.net Fri Mar 14 11:18:01 2008
From: "James Gary Prudhomme jprudhomme(0)healthtech.com" <owner-chemistry*o*server.ccl.net>
To: CCL
Subject: CCL: Structure-Based Drug Design - Conference Early Bird Rate expires 4/11
Message-Id: <-36501-080314111520-22016-bLHr8ftGhfwSK+wGYgxfQQ*o*server.ccl.net>
X-Original-From: "James Gary Prudhomme" <jprudhomme^^^healthtech.com>
Date: Fri, 14 Mar 2008 11:15:15 -0400
Sent to CCL by: "James Gary Prudhomme" [jprudhomme**healthtech.com]
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From owner-chemistry@ccl.net Fri Mar 14 11:52:00 2008
From: "Dan Maftei dan.maftei]~[chem.uaic.ro" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: BABEL, Z-matrix, modredundant?
Message-Id: <-36502-080314113849-2240-Zth+j6hYDj9Szpw3PNEBUw..server.ccl.net>
X-Original-From: Dan Maftei <dan.maftei|a|chem.uaic.ro>
Content-Type: multipart/mixed;
boundary="------------060304060602040108010903"
Date: Fri, 14 Mar 2008 17:06:28 +0200
MIME-Version: 1.0
Sent to CCL by: Dan Maftei [dan.maftei%x%chem.uaic.ro]
This is a multi-part message in MIME format.
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The short answer is Yes. You may read the long answer here:
http://www.gaussian.com/g_gv/gv3/modred.htm.
The frozen coordinate (distance, angle, dihedral) should be added (after
a blank line) at the end of your cartezian atomic definitions. To
freeze, for example, the torsion angle between atoms 1,2,3 and 4 one
sould add:
D 1 2 3 4 F
(D-meaning dihedral, F-meaning frozen)
Consequently, the # route section must contain opt=modredundant or
opt(modredundant,...).
After initialization, in the "Initial Parameters" table, check for the
"Frozen" word in log file (column labeled "Derivative Info.").
David Close closed##etsu.edu wrote:
> Sent to CCL by: "David Close" [closed]^[etsu.edu]
> I've just installed the new version of BABEL, and have noted that I can't get a z-matrix from the sleected outputs. My old version (DOS) was able to convert crysallographic coordinates directly into Gaussian z-matrix output.
> I have always used the z-matrix input to Gaussian jobs when I wanted to freeze some coordinates. But last week there was a discussion on this list on whether or not it is necessary to use a z-matrix if one wants to freeze coordinates using modredundant. I can't seem to find the response to this question.
> So my question is, if I can't make BABEL convert an output to a z-matrix,
> can I use the normal xyz coordinates and freeze a torsion angle with the Modredundant command?
> Regards, Dave Close.>
>
>
>
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From owner-chemistry@ccl.net Fri Mar 14 13:51:01 2008
From: "Minhaj mmg016(0)gmail.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL:G: BABEL, Z-matrix, modredundant?
Message-Id: <-36503-080314095241-31449-ixkCTrP3PoL0qHNzRisrCw() server.ccl.net>
X-Original-From: Minhaj <mmg016]=[gmail.com>
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Date: Fri, 14 Mar 2008 07:49:38 -0500
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Sent to CCL by: Minhaj [mmg016(a)gmail.com]
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You can fix the atomic positions in gaussian jobs when when you use XYZ
coordinates, but I dont think you can fix a torsion angle.
On Fri, Mar 14, 2008 at 7:09 AM, David Close closed##etsu.edu <
owner-chemistry(0)ccl.net> wrote:
>
> Sent to CCL by: "David Close" [closed]^[etsu.edu]
> I've just installed the new version of BABEL, and have noted that I can't
> get a z-matrix from the sleected outputs. My old version (DOS) was able to
> convert crysallographic coordinates directly into Gaussian z-matrix output.
> I have always used the z-matrix input to Gaussian jobs when I wanted to
> freeze some coordinates. But last week there was a discussion on this list
> on whether or not it is necessary to use a z-matrix if one wants to freeze
> coordinates using modredundant. I can't seem to find the response to this
> question.
> So my question is, if I can't make BABEL convert an output to a z-matrix,
> can I use the normal xyz coordinates and freeze a torsion angle with the
> Modredundant command?
> Regards, Dave Close.>
>
>
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You can fix the atomic positions in gaussian jobs when when you use XYZ coordinates, but I dont think you can fix a torsion angle.<br><br><div class="gmail_quote">On Fri, Mar 14, 2008 at 7:09 AM, David Close closed##etsu.edu <<a href="mailto:owner-chemistry(0)ccl.net">owner-chemistry(0)ccl.net</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: "David Close" [closed]^[<a href="http://etsu.edu" target="_blank">etsu.edu</a>]<br>
I've just installed the new version of BABEL, and have noted that I can't get a z-matrix from the sleected outputs. My old version (DOS) was able to convert crysallographic coordinates directly into Gaussian z-matrix output.<br>
I have always used the z-matrix input to Gaussian jobs when I wanted to freeze some coordinates. But last week there was a discussion on this list on whether or not it is necessary to use a z-matrix if one wants to freeze coordinates using modredundant. I can't seem to find the response to this question.<br>
So my question is, if I can't make BABEL convert an output to a z-matrix,<br>
can I use the normal xyz coordinates and freeze a torsion angle with the Modredundant command?<br>
Regards, Dave Close.<br>
<br>
<br>
<br<br<br<br<br>
<br>
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From owner-chemistry@ccl.net Fri Mar 14 14:26:00 2008
From: "Geoffrey Hutchison geoffh+]![pitt.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL:G: BABEL, Z-matrix, modredundant?
Message-Id: <-36504-080314113053-28659-zwkDwrlmTdzbO2VyndkGsA---server.ccl.net>
X-Original-From: Geoffrey Hutchison <geoffh+:pitt.edu>
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Sent to CCL by: Geoffrey Hutchison [geoffh+_._pitt.edu]
On Mar 14, 2008, at 8:09 AM, David Close closed##etsu.edu wrote:
> I've just installed the new version of BABEL, and have noted that I
> can't get a z-matrix from the sleected outputs. My old version
> (DOS) was able to convert crysallographic coordinates directly into
> Gaussian z-matrix output.
File formats are added to Open Babel all the time. However, since Open
Babel is a volunteer project, they also tend to be added when current
developers need them, or someone contributes the code. In this case, I
can say that the latest beta snapshots of Open Babel 2.2 contain
Gaussian z-matrix output. This was requested by a colleague.
Please give it a try -- source code is available:
http://sourceforge.net/project/showfiles.php?group_id=40728&package_id=154019
Of course, Open Babel also has its own mailing lists, including places
to suggest features and new file formats -- there's no need to clutter
CCL.net. Contributions and suggestions are always welcome!
http://openbabel.org/
Cheers,
-Geoff
From owner-chemistry@ccl.net Fri Mar 14 15:01:00 2008
From: "Boobalan Pachaiyappan boobalanp##gmail.com" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: ROC curve
Message-Id: <-36505-080311142641-17599-rkzwAY252jNvTmpHSalGBQ ~~ server.ccl.net>
X-Original-From: "Boobalan Pachaiyappan" <boobalanp%a%gmail.com>
Date: Tue, 11 Mar 2008 14:26:37 -0400
Sent to CCL by: "Boobalan Pachaiyappan" [boobalanp**gmail.com]
Hello All,
I'm wondering whether there is any free software(s) for academic researchers to perform ROC curve analysis. Your response is highly appreciated.
Boobalan
(UIC)
From owner-chemistry@ccl.net Fri Mar 14 15:36:00 2008
From: "N. Sukumar nagams-#-rpi.edu" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: Elegantly Describing Molecules with a Certain Geometric Property
Message-Id: <-36506-080314123223-19135-FeQQSPR+uYXItaQeoOIX6Q-x-server.ccl.net>
X-Original-From: "N. Sukumar" <nagams[#]rpi.edu>
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Date: Fri, 14 Mar 2008 11:31:32 -0400
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Sent to CCL by: "N. Sukumar" [nagams..rpi.edu]
I think you're describing symmetry with respect to the permutation group rather than a point group symmetry. The totally symmetric group you want is Sn where n is the index in XYn or Xn molecules. According to Wikipedia http://en.wikipedia.org/wiki/Permutation_group and http://en.wikipedia.org/wiki/Symmetric_group if M is any finite or infinite set, then the group of all permutations of M is written as Sym(M).
N. Sukumar
Associate Research Professor of Chemistry and Chemical Biology
Center for Biotechnology and Interdisciplinary Studies
Rensselaer Polytechnic Institute
http://reccr.chem.rpi.edu/
==============Original message text===============
On Fri, 14 Mar 2008 7:21:49 EDT "Matthew Thompson
matthew.thompson.:.nrl.navy.mil" wrote:
Sent to CCL by: Matthew Thompson [matthew.thompson#nrl.navy.mil]
Folks, I'm hoping there is a group theory savant or someone on this list
who can help me with a puzzle of mine. Namely, I'm trying to figure out
the best or most concise way to describe a set of molecules, maybe, if
possible, in group theoretical terms.
The set I'm looking at is the set of all uni- and di-elemental molecules
that have *one* representative bond length. Obvious examples are all XY
and all X2 molecules; likewise, H2O, CH4, and SF6 also have one
characteristic bond length.
Thus, I've been wondering if there was some way to describe these
molecules in a concise way with group theory. I can't say all Cnv and
Dnh work since N2O kills that (needs rNN and rNO to describe). I can't
say their point group must be Abelian because of Td and Oh (CH4 and SF6).
I think you could couch it in Z-matrix terms by saying you only need one
distance no matter the length of the Z-matrix (i.e., only one number in
the third column), but that seems sort of inelegant. It seems like
there must be some way to do this but I just can't figure it out. So, I
thought I'd ask CCL and probably get an answer in an instant.
Thanks for any help,
Matt
--
Matt Thompson, PhD
Naval Research Laboratory
202-767-2160http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========
From owner-chemistry@ccl.net Fri Mar 14 16:11:01 2008
From: "Carlos Simmerling carlos.simmerling|a|gmail.com" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Space still available in ACS Emerging Technology $1000 competition
Message-Id: <-36507-080314153458-25978-WSzWhcrlkseIgu0M8TB9VQ*_*server.ccl.net>
X-Original-From: "Carlos Simmerling" <carlos.simmerling#,#gmail.com>
Date: Fri, 14 Mar 2008 15:34:55 -0400
Sent to CCL by: "Carlos Simmerling" [carlos.simmerling!=!gmail.com]
Space is still available in this symposium!
please submit your abstracts before the March 17th OASYS deadline.
We encourage people to enter any new technology related to computational
chemistry. We also welcome work describing development of new methods or significant modifications to existing methods, or any other developments that will facilitate research in the computational chemistry community.
$1,000 prize to be awarded at the ACS national meeting, Philadelphia, PA.
The Computers in Chemistry Division (COMP) of the ACS will hold the
annual Symposium on Emerging Technologies in Computational Chemistry at
the American Chemical Society National Meeting, Philadelphia, PA, Aug.
17-21 2008. The objective of the symposium is to stimulate, reward, and
publicize methodological advances in computational chemistry.
The talks will be evaluated at the meeting by a panel of experts on the
quality of the presentation, and the impact that the research will have
on the future of computational chemistry and allied sciences. The
symposium is ideal for presenting your latest and best research on new
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Schrodinger, Inc., sponsors a $1,000 prize for the best talk at the symposium.
All are invited to participate. To participate, it is necessary to submit a regular short ACS abstract via http://oasys.acs.org/ . It is also necessary to also email a longer (~1000-word) abstract to the organizer. The talks must be original and not be repeats of talks at other ACS symposia. The long abstracts will be evaluated, and those individuals selected for an oral presentation at the symposium will be notified. Applications for the Emerging Technologies Symposium that cannot be accepted will be rescheduled in one of the other COMP sessions at the meeting.
Long abstracts must be sent by e-mail to
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Please use a subject of "ACS Emerging Tech Abstract".
The short abstract must be submitted to OASYS by the normal deadline of
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Carlos Simmerling
Chair, ACS COMP Division Awards Committee
Professor, Department of Chemistry
Stony Brook University
Stony Brook, NY 11794-3400
631-632-1336
From owner-chemistry@ccl.net Fri Mar 14 16:45:00 2008
From: "Michel PETITJEAN michel.petitjean%%cea.fr" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: RE : Elegantly Describing Molecules with a Certain Geometric Property
Message-Id: <-36508-080314121427-7794-yrRxjbvJtcRwTJeHponNoQ|server.ccl.net>
X-Original-From: "Michel PETITJEAN" <michel.petitjean..cea.fr>
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Do you mean: given the point group symmetry class and the representative =
bond length
then you would be able to generate the cartesian coordinates, up to a =
direct isometry ?
It seems to me that sulphur rings (Sn) have a representative bond length
although torsonial angles may vary.
May be you could refine the definition of the class of molecules that
you are considering.
Best regards,
Michel Petitjean,
DSV/iBiTec-S/SB2SM (CNRS URA 2096)
CEA Saclay, bat. 528
91191 Gif-sur-Yvette Cedex
Phone: +33(0)1 6908 4006 / Fax: +33(0)1 6908 4007
E-mail: michel.petitjean[A]cea.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.html
-------- Message d'origine--------
De: Matthew Thompson matthew.thompson.:.nrl.navy.mil =
[mailto:owner-chemistry[A]ccl.net]
Date: ven. 14/03/2008 12:21
=C0: Michel PETITJEAN
Objet : CCL: Elegantly Describing Molecules with a Certain Geometric =
Property
=20
Sent to CCL by: Matthew Thompson [matthew.thompson#nrl.navy.mil]
Folks, I'm hoping there is a group theory savant or someone on this list =
who can help me with a puzzle of mine. Namely, I'm trying to figure out =
the best or most concise way to describe a set of molecules, maybe, if=20
possible, in group theoretical terms.
The set I'm looking at is the set of all uni- and di-elemental molecules =
that have *one* representative bond length. Obvious examples are all XY =
and all X2 molecules; likewise, H2O, CH4, and SF6 also have one=20
characteristic bond length.
Thus, I've been wondering if there was some way to describe these=20
molecules in a concise way with group theory. I can't say all Cnv and=20
Dnh work since N2O kills that (needs rNN and rNO to describe). I can't =
say their point group must be Abelian because of Td and Oh (CH4 and =
SF6).
I think you could couch it in Z-matrix terms by saying you only need one =
distance no matter the length of the Z-matrix (i.e., only one number in=20
the third column), but that seems sort of inelegant. It seems like=20
there must be some way to do this but I just can't figure it out. So, I =
thought I'd ask CCL and probably get an answer in an instant.
Thanks for any help,
Matt
--=20
Matt Thompson, PhD
Naval Research Laboratory
202-767-2160
-=3D This is automatically added to each message by the mailing script =
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search)http://www.ccl.net/spammers.txt------_=_NextPart_001_01C885E3.F1FD2E11--
From owner-chemistry@ccl.net Fri Mar 14 17:20:01 2008
From: "Iain Wallace iain.m.wallace=-=gmail.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: SAR software
Message-Id: <-36509-080314165437-6218-u2nYegaYdw6e5JTUWQsuKA]=[server.ccl.net>
X-Original-From: "Iain Wallace" <iain.m.wallace_-_gmail.com>
Content-Type: multipart/alternative;
boundary="----=_Part_1518_32613090.1205524686685"
Date: Fri, 14 Mar 2008 15:58:06 -0400
MIME-Version: 1.0
Sent to CCL by: "Iain Wallace" [iain.m.wallace=gmail.com]
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Hi all,
Just wondering if anybody could recommend any (free/trialware) software for
viewing sets of compounds when generating Structure Activity Relationships.
Is there an automatic way of viewing each molecule with a core structure and
R groups? (I know Pipeline pilot has an option for this, but I won't have
access to it for the next week or so)
Thanks :)
Iain
------=_Part_1518_32613090.1205524686685
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Hi all,<br><br>Just wondering if anybody could recommend any (free/trialware) software for viewing sets of compounds when generating Structure Activity Relationships.<br>Is there an automatic way of viewing each molecule with a core structure and R groups? (I know Pipeline pilot has an option for this, but I won't have access to it for the next week or so)<br>
<br>Thanks :)<br><br>Iain<br><br>
------=_Part_1518_32613090.1205524686685--
From owner-chemistry@ccl.net Fri Mar 14 17:56:01 2008
From: "Jana Precechtelova janap(!)ncbr.chemi.muni.cz" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL:G: mpshift with COSMO in Turbomole?
Message-Id: <-36510-080314170514-16273-5uyWPV54/ggZpcqh5V1YNA : server.ccl.net>
X-Original-From: Jana Precechtelova <janap _ ncbr.chemi.muni.cz>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Fri, 14 Mar 2008 21:01:12 +0100 (MET)
MIME-Version: 1.0
Sent to CCL by: Jana Precechtelova [janap!A!ncbr.chemi.muni.cz]
Hi CCLers,
Does anybody happen to know if it is possible to run calculations of NMR
chemical shifts in the presence of COSMO solvent in Turbomole? That is -
are GIAO / COSMO coupling terms implemented in Turbomole?
I know it's available in g03 but g03 is rather slow for my purpose ...
Thanks a lot
Regards,
Jana
=============================================================
Jana Precechtelova
-------------------------------------------------------------
NMR Laboratory
National Centre for Biomolecular Research (NCBR)
Faculty of Science, Masaryk University
Kamenice 3, 625 00 Brno, Czech Republic
=============================================================
email: janap]|[ncbr.chemi.muni.cz
=============================================================