From owner-chemistry@ccl.net Thu Nov 16 05:11:00 2006
From: "Tatsis A Vasileios me01136++cc.uoi.gr" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: couple AM1 and Molecular Dynamics
Message-Id: <-33042-061116050247-24902-dy/YMzUo1WZFWld2orMTWA^^server.ccl.net>
X-Original-From: "Tatsis A Vasileios" <me01136 a cc.uoi.gr>
Date: Thu, 16 Nov 2006 05:02:47 -0500


Sent to CCL by: "Tatsis A Vasileios" [me01136]~[cc.uoi.gr]
Hello to all CCLers!!!

I, recently, managed to couple two well known packages in order to get quantum molecular dynamics trajectories.
I am trying to find a way so i can validate my results(trajectories), (publications, other free software).

Thanks in advance


From owner-chemistry@ccl.net Thu Nov 16 08:22:00 2006
From: "kubicki**geosc.psu.edu" <owner-chemistry/./server.ccl.net>
To: CCL
Subject: CCL: OH radical attack to aromatic compounds
Message-Id: <-33043-061116072222-20411-rBPBFXdK2UEHKeWiLLcBpw/./server.ccl.net>
X-Original-From: kubicki=geosc.psu.edu
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Date: Thu, 16 Nov 2006 06:24:30 -0500 (EST)
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Sent to CCL by: kubicki(~)geosc.psu.edu
You should look at the work of James Rabinowitz of EPA.
He has done a lot of work on computing the oxidation of
aromatics.

> Sent to CCL by: Jimmy Lawrence [jlawrence~!~slb.com]
> Dear all,
>
>  I would like to do some calculations regarding free radical attack (e.g.
> OH
> free radical ) to aromatic compounds to find its preference and easiness
> to
> attack on aromatic ring (attack location). Right now I think IRC
> calculation
> might help this.
> Can you share any experiences/ suggest methods for this kind of
> calculation
> ? Since calculating system with free radical might be tricky, should I
> start
>> from H2O2, for example ?
>
> Thank you in advance,
>
> Jimmy Lawrence>
>
>
>


From owner-chemistry@ccl.net Thu Nov 16 08:56:01 2006
From: "Ramon Crehuet rcsqtc^iiqab.csic.es" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: couple AM1 and Molecular Dynamics
Message-Id: <-33044-061116081004-29768-DvEGgJYaFwvd93ROUU44Vw**server.ccl.net>
X-Original-From: Ramon Crehuet <rcsqtc[a]iiqab.csic.es>
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Date: Thu, 16 Nov 2006 13:19:49 +0100
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Sent to CCL by: Ramon Crehuet [rcsqtc-.-iiqab.csic.es]
Dear Tatsis,
You can try DYNAMO, which specifically includes AM1 and Molecular 
Dynamics (Verlet, Langevin,...).
http://www.ibs.fr/ext/labos/LDM/projet6/Main.html

Regards,
Ramon



Tatsis A Vasileios me01136++cc.uoi.gr wrote:

>Sent to CCL by: "Tatsis A Vasileios" [me01136]~[cc.uoi.gr]
>Hello to all CCLers!!!
>
>I, recently, managed to couple two well known packages in order to get quantum molecular dynamics trajectories.
>I am trying to find a way so i can validate my results(trajectories), (publications, other free software).
>
>Thanks in advance>
>
>
>
>  
>


From owner-chemistry@ccl.net Thu Nov 16 09:31:00 2006
From: "axel axbchb .. gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian03 D02 problems in SGI Altix ia64
Message-Id: <-33045-061116072649-20711-ggSUbLwqKNnxTUQE7yTpPQ^server.ccl.net>
X-Original-From: axel <axbchb]-[gmail.com>
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Date: Thu, 16 Nov 2006 12:21:15 +0100
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Sent to CCL by: axel [axbchb^_^gmail.com]
Dear all,


I've compiled Gaussian03 revision D02 in an SGI Altix machine
with ia64 processors using the ifort an icc compilers version 9.0
and MKL librarires version 8.0.

Thought the compilation ends fine, there are some problems
with the PCM solvent model calculations. These stop suddenly
when building up the cavity without any error message.

Has anyone come through this problem? Has anyone
managed to solve it?

Thanks in advance,


Axel Bidon-Chanal
Faculty of Pharmacy
University of Barcelona


From owner-chemistry@ccl.net Thu Nov 16 11:45:00 2006
From: "Gustavo Seabra gustavo.seabra^_^gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: couple AM1 and Molecular Dynamics
Message-Id: <-33046-061116105927-8147-PGNVlwhoNX3JHRtUlg/lWQ^server.ccl.net>
X-Original-From: "Gustavo Seabra" <gustavo.seabra^gmail.com>
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Sent to CCL by: "Gustavo Seabra" [gustavo.seabra(~)gmail.com]
Hi,

You could try the Amber molcular dynamics package. In it's latest
version (Amber 9), it includes many differnt semi empirical methods,
like AM1, PM3 and SCC-DFTB.

HTH

Gustavo.

On 11/16/06, Tatsis A Vasileios me01136++cc.uoi.gr
<owner-chemistry{}ccl.net> wrote:
> Sent to CCL by: "Tatsis A Vasileios" [me01136]~[cc.uoi.gr]
> Hello to all CCLers!!!
>
> I, recently, managed to couple two well known packages in order to get quantum molecular dynamics trajectories.
> I am trying to find a way so i can validate my results(trajectories), (publications, other free software).
>
> Thanks in advance


From owner-chemistry@ccl.net Thu Nov 16 15:23:00 2006
From: "Da Gao dagao06{=}gmail.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Cartesian coordinates to Z-Matrix
Message-Id: <-33047-061116142555-26457-dptICmaajcF4SbQRZJHVMA*server.ccl.net>
X-Original-From: "Da Gao" <dagao06[A]gmail.com>
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Date: Thu, 16 Nov 2006 11:22:16 -0700
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Sent to CCL by: "Da Gao" [dagao06,+,gmail.com]
------=_Part_125354_27878444.1163701336195
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Dear all,

Is anyone here be aware of the software that can transfer Cartesian
coordinates to Z-Matrix ? Thanks for sharing.

-- 
Best Regards,

Da

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Dear all,<br><br>Is anyone here be aware of the software that can transfer Cartesian coordinates to Z-Matrix ? Thanks for sharing.<br clear="all"><br>-- <br>Best Regards,<br><br>Da

------=_Part_125354_27878444.1163701336195--


From owner-chemistry@ccl.net Thu Nov 16 21:19:00 2006
From: "carlito jr. ponseca sagespres2002,+,yahoo.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: frequency scaling in GAMESS...
Message-Id: <-33048-061116044855-24011-I9k0TlgvhHkWJmFztNg5VQ[*]server.ccl.net>
X-Original-From: "carlito jr. ponseca" <sagespres2002 ~ yahoo.com>
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Date: Thu, 16 Nov 2006 00:48:40 -0800 (PST)
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Sent to CCL by: "carlito jr. ponseca" [sagespres2002%x%yahoo.com]

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I am using PCGAMESS. The calculation results seem to fit well with our expe=
rimental data after I have scaled the frequency (.9085 for HF321G). However=
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cal factor is indeed acceptable especially in lower frequency region of the=
 spectrum (30 cm-1 to 230 cm-1).=0A =0AThank you very much and I will be wa=
iting for your response.=0A =0ASincerely,=0A =0ACarl=0A=0A=0A--------------=
------------------------------------------------=0Aengr. carlito s. ponseca=
 jr=0Aphd student=0Adepartment of functional molecular science=0Aschool of =
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ad><body><div style=3D"font-family:arial, helvetica, sans-serif;font-size:1=
0pt"><DIV></DIV>=0A<DIV>=0A<DIV>=0A<DIV>I am&nbsp;using PCGAMESS.&nbsp;The =
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like to know&nbsp;what references I can&nbsp;cite to prove that&nbsp;such e=
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From owner-chemistry@ccl.net Thu Nov 16 21:53:01 2006
From: "Nuno A. G. Bandeira nuno.bandeira!^!ist.utl.pt" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Cartesian coordinates to Z-Matrix
Message-Id: <-33049-061116165521-25781-zgh25tqwrZSEExbjTO2RLw++server.ccl.net>
X-Original-From: "Nuno A. G. Bandeira" <nuno.bandeira%ist.utl.pt>
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Date: Thu, 16 Nov 2006 21:55:09 +0000
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Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira\a/ist.utl.pt]

Da Gao dagao06{=}gmail.com wrote:
> Sent to CCL by: "Da Gao" [dagao06,+,gmail.com]
> ------=_Part_125354_27878444.1163701336195
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Content-Transfer-Encoding: 7bit
> Content-Disposition: inline
> 
> Dear all,
> 
> Is anyone here be aware of the software that can transfer Cartesian
> coordinates to Z-Matrix ? Thanks for sharing.
> 

Yes, you can use openbabel to convert from xyz coordinates to 
Fenske-Hall (Gaussian) Z-Matrix.

Regards,

-- 
Nuno A. G. Bandeira, AMRSC
Graduate researcher and molecular sculptor
Inorganic and Theoretical Chemistry Group,
Faculty of Science
University of Lisbon - C8 building, Campo Grande,
1749-016 Lisbon,Portugal
http://cqb.fc.ul.pt/intheochem/nuno.html
Doctoral student (-) IST,Lisbon
--