From chemistry-request@ccl.net Thu Oct 28 04:42:36 2004
Received: from gveu50.emea.givaudan.com ([57.68.15.178])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9S9gZpH002962;
	Thu, 28 Oct 2004 04:42:35 -0500
To: korkin[at]nanoandgiga.com
Cc: chemistry[at]ccl.net,
   "Computational Chemistry List" <chemistry-request[at]ccl.net>
Subject: Re: CCL:semi-emprical QM compter program for periodic systems?
MIME-Version: 1.0
X-Mailer: Lotus Notes Release 5.0.11   July 24, 2002
Message-ID: <OF6A8F35F5.2CB0D54A-ONC1256F3B.0035FC5E-C1256F3B.00367DD8[at]emea.givaudan.com>
From: andras.borosy[at]givaudan.com
Date: Thu, 28 Oct 2004 11:55:11 +0200
X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12  |February 13, 2003) at
 28/10/2004 11:55:17,
	Serialize complete at 28/10/2004 11:55:17
Content-Type: text/plain; charset="iso-8859-1"
X-Spam-Status: No, hits=5.3 required=7.5 tests=FVGT_s_OBFU_Q1,IMPRONONCABLE_1,
	NO_RDNS2,NO_REAL_NAME autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9S9gapH002966

Dear Mr. Korkin,

Try CAChe (http://www.cachesoftware.com/cache/index.shtml)!

Regards,

Dr. Andras Borosy





korkin[at]nanoandgiga.com
Sent by: "Computational Chemistry List" <chemistry-request[at]ccl.net>
26.10.2004 19:36

 
        To:     chemistry[at]ccl.net
        cc: 
        Subject:        CCL:semi-emprical QM compter program for periodic systems?


Dear Coleagues,

I am looking for the software program(s) to describe periodic systems (not
molecuar type clusters!) such as Si-SiO2 interfaces on the level of
semi-empirical quantum chemistry. There are plenty of different empirical
force fileds which obviously work in a very narrow area of application
limited for classical mechannics and there are numbers of ab-initio (or ab
initio like for those who want to distibguish these two definitions) DFT
codes but there is seems to be a shortage of unexpensive QM methods and
computer programs (!) for periodic systems, which are based on or similar
to NDDO based methods popular in the molecular world. Transition metal
systems or ionic crystals are not well suited for NDDO type methods while
Si-SiO2 is on the edge and I believe some NDDO-like methods may still be
cheap enough and reasonable enough as a first approximation for a variaety
of properties accessible for QM methods within one calucation [including
geometry optimization] such as strcture, geometry and electronic
properties. Any pointers to the software programs of this kind will be
very much appreciated as well as general advises and comments.

If there is enough interest I will send my summary back to CCL.
Since I am not at the CCL list and watch it only via web interface,
please, copy your response directly to me to my yahoo e-mail
( a_korkin[at]yahoo.com )

Best regards,
Anatoli Korkin
a_korkin[at]yahoo.com

-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: 
line
and send your message to:  CHEMISTRY[at]ccl.net

Send your subscription/unsubscription requests to: 
CHEMISTRY-REQUEST[at]ccl.net 
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow[at]nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+











From chemistry-request@ccl.net Thu Oct 28 02:47:45 2004
Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9S7lfpH029983
	for <CHEMISTRY/at/ccl.net>; Thu, 28 Oct 2004 02:47:44 -0500
Received: by lgdx04.lg.ehu.es id KAA0000001511; Thu, 28 Oct 2004 10:00:09 +0200 (MET DST)
Message-ID: <004401c4bcc4$27873200$222fe39e/at/lc.ehu.es>
From: "Pablo Vitoria" <qibvigap/at/lg.ehu.es>
To: "raquel crespin" <rache97/at/yahoo.com>, "CCL" <CHEMISTRY/at/ccl.net>
References: <20041027145714.18264.qmail/at/web14126.mail.yahoo.com>
Subject: Re: CCL:About  Scratch usage in Gaussian
Date: Thu, 28 Oct 2004 10:00:09 +0200
MIME-Version: 1.0
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: 8bit
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 6.00.2800.1437
X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1441
X-Spam-Status: No, hits=1.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR 
	autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net

Hi Rachel,

As 335803017 words is 2.5 GB, you are hitting the 2GB file limit which was
usual in Windows or Linux systems. You have two options.If  you have access
to the source code, you can recompile it with large file support (it can be
done with g03 in Linux, I don4t know about g98 or other OS). If you don4t,
you can split the .rwf in several parts using Link0 commands that must be at
the beginning of your input file. For example, if you use /scratch as your
scratch directory, you can split your .rwf file in two parts of less tan 2GB
each including:

%rwf=/scratch/1.rwf,245MW,/scratch/2.rwf,245MW

I copy below from the g03 manual:

%RWF=loc1,size1,loc2,size2, ...
An alternate syntax is provided for splitting the Read-Write file among two
or more disks (or file systems). Each location is followed by a maximum size
for the file segment at that location. The default units for each size is
words; the value may be optionally followed by KB, MB, GB, KW, MW or GW
(with no intervening spaces) to indicate units. A value of -1 for any size
parameter indicates that any and all available space may be used, and a
value of 0 indicates that an existing segment should retain its current
size. The locations may be either directory locations, or full pathnames.
Note that directory specifications must include terminal slashes (on UNIX
systems).

Pablo

--------------------------------------------------------
Pablo Vitoria Garcia
Dpto. Qummica Inorganica, Facultad de Ciencias
Universidad del Pams Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)

Tfno. 94 6015992
Fax. 94 6013500
----- Original Message ----- 
From: "raquel crespin" <rache97/at/yahoo.com>
To: <chemistry/at/ccl.net>
Sent: Wednesday, October 27, 2004 4:57 PM
Subject: CCL:About Scratch usage in Gaussian


| Hello CCL members!
| I tried to run MP2/aug-cc-pVTZ calculation with g98,
| my system have 7 atoms (230 basis functions and 333
| primitives) and after few minutes the following
| message appears:
| Estimated scratch disk usage=   336257611 words.
|  Actual    scratch disk usage=   335803017 words.
|  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
|  Actual    scratch disk usage=   335802069 words.
| Erroneous write during file extend. write 61632511
| instead of 4096
| Probably out of disk space.
|  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
|  Actual    scratch disk usage=   335802069 words.
| Erroneous write during file extend. write 61632511
| instead of 4096
| Probably out of disk space.
|  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
|  Actual    scratch disk usage=   335802069 words.
| Erroneous write during file extend. write 61632511
| instead of 4096
| Probably out of disk space.
|  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
|  Actual    scratch disk usage=   335802069 words.
| Erroneous write during file extend. write 61632511
| instead of 4096
| Probably out of disk space.
|  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
|  Actual    scratch disk usage=   335802069 words.
| Erroneous write during file extend. write 61632511
| instead of 4096
| Probably out of disk space.
| and the calculation stops. I change %mem, %Maxdisk and
| test with direct procedure, but the problem continues.
| What can I do in this case?
| Thanks
| Rachel
|
|
|
| __________________________________
| Do you Yahoo!?
| Take Yahoo! Mail with you! Get it on your mobile phone.
| http://mobile.yahoo.com/maildemo
|
|
| -= This is automatically added to each message by the mailing script =-
| To send e-mail to subscribers of CCL put the string CCL: on your Subject:
line
| and send your message to:  CHEMISTRY/at/ccl.net
|
| Send your subscription/unsubscription requests to:
CHEMISTRY-REQUEST/at/ccl.net
| HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs
|
| If your mail is bouncing from CCL.NET domain send it to the maintainer:
| Jan Labanowski,  jlabanow/at/nd.edu (read about it on CCL Home Page)
| -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
|
|
|
|
|
|



From chemistry-request@ccl.net Thu Oct 28 04:36:55 2004
Received: from gveu50.emea.givaudan.com ([57.68.15.178])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9S9arpH002780;
	Thu, 28 Oct 2004 04:36:54 -0500
To: avw1557!at!ksu.edu
Cc: chemistry!at!ccl.net,
   "Computational Chemistry List" <chemistry-request!at!ccl.net>
Subject: Re: CCL:predicting circular dichroism spectra
MIME-Version: 1.0
X-Mailer: Lotus Notes Release 5.0.11   July 24, 2002
Message-ID: <OFA72649F4.7EACC721-ONC1256F3B.0035D322-C1256F3B.0035F9B4!at!emea.givaudan.com>
From: andras.borosy!at!givaudan.com
Date: Thu, 28 Oct 2004 11:49:33 +0200
X-MIMETrack: Serialize by Router on gvedoh01/H/Givaudan(Release 5.0.12  |February 13, 2003) at
 28/10/2004 11:49:35,
	Serialize complete at 28/10/2004 11:49:35
Content-Type: text/plain; charset="iso-8859-1"
X-Spam-Status: No, hits=5.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR,NO_RDNS2,
	NO_REAL_NAME autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9S9atpH002784

Dear Mr. Wiznycia,

Try Turbomole!. It is capable to calculate optical rotation, and much 
faster the Gaussian.

Regards,

Dr. Andras Borosy





avw1557!at!ksu.edu
Sent by: "Computational Chemistry List" <chemistry-request!at!ccl.net>
27.10.2004 02:59

 
        To:     chemistry!at!ccl.net
        cc: 
        Subject:        CCL:predicting circular dichroism spectra


Hello all,

I have recently begun working with salen type compounds and would like
to run calculations to predict UV/CD spectra to compare to the
experimental data.  Does anyone have experience with commercially
available software (e.g. gaussian 03) and could recommend a good
software package to use, and if possible what would be the best
software package to use.  We are looking to purchase one.

Thanks

Alex Wiznycia
Department of Chemistry
Kansas State University
111 Willard Hall
Manhattan KS 66506-3701
email : avw1557!at!ksu.edu


-= This is automatically added to each message by the mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: 
line
and send your message to:  CHEMISTRY!at!ccl.net

Send your subscription/unsubscription requests to: 
CHEMISTRY-REQUEST!at!ccl.net 
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jlabanow!at!nd.edu (read about it on CCL Home Page)
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+











From chemistry-request@ccl.net Thu Oct 28 05:33:23 2004
Received: from rinka.central.susx.ac.uk (rinka.central.susx.ac.uk [139.184.14.19])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9SAXMpH004821
	for <chemistry..at..ccl.net>; Thu, 28 Oct 2004 05:33:23 -0500
Received: from dorothy.mols.susx.ac.uk ([139.184.113.152])
	by rinka.central.susx.ac.uk with esmtp (Exim 4.10)
	id 1CN7nA-0000k5-00; Thu, 28 Oct 2004 11:46:04 +0100
Date: Thu, 28 Oct 2004 11:45:53 +0100
To: raquel crespin <rache97..at..yahoo.com>, chemistry..at..ccl.net
Subject: Re: CCL:About  Scratch usage in Gaussian
Message-ID: <770000.1098960353..at..dorothy.mols.susx.ac.uk>
In-Reply-To: <20041027145714.18264.qmail..at..web14126.mail.yahoo.com>
References:  <20041027145714.18264.qmail..at..web14126.mail.yahoo.com>
Originator-Info: login-token=Mulberry:01xzHk5S6VR0bsYSdSJJAzX1daLaRMXfGIKl9ZUA==;
 token_authority=support..at..sussex.ac.uk
X-Mailer: Mulberry/3.0.3 (Linux/x86)
MIME-Version: 1.0
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit
Content-Disposition: inline
X-Sussex: true
From: Georgina Aitken <g.d.c.aitken..at..sussex.ac.uk>
X-Spam-Status: No, hits=4.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR,NO_RDNS2 
	autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net

Dear Raquel,

you could try splitting up the rwf files that are generated during the 
calculation as these usually use the most memory.
On the first line of your input file give the directory where the .rwf 
files are generated (e.g. work) followed by a the file names for each rwf 
file (e.g scratch1):

%RWF=/work/scratch1,1900MB,/work/scratch2,1900MB,/work/scratch3,1900MB,/wor
k/scratch4,1900MB
%NoSave
%chk=etc.chk
....

You can generate as many rwf files as necessary.
So that these files are automatically deleted once the calc has finished I 
put %Nosave command on the second line of my input file followed by the 
rest of the input for the calculation.

Georgina Aitken

--On Wednesday, October 27, 2004 07:57:14 -0700 raquel crespin 
<rache97..at..yahoo.com> wrote:

> Hello CCL members!
> I tried to run MP2/aug-cc-pVTZ calculation with g98,
> my system have 7 atoms (230 basis functions and 333
> primitives) and after few minutes the following
> message appears:
> Estimated scratch disk usage=   336257611 words.
>  Actual    scratch disk usage=   335803017 words.
>  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
>  Actual    scratch disk usage=   335802069 words.
> Erroneous write during file extend. write 61632511
> instead of 4096
> Probably out of disk space.
>  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
>  Actual    scratch disk usage=   335802069 words.
> Erroneous write during file extend. write 61632511
> instead of 4096
> Probably out of disk space.
>  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
>  Actual    scratch disk usage=   335802069 words.
> Erroneous write during file extend. write 61632511
> instead of 4096
> Probably out of disk space.
>  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
>  Actual    scratch disk usage=   335802069 words.
> Erroneous write during file extend. write 61632511
> instead of 4096
> Probably out of disk space.
>  IMap=  1  2  3  4 13  5 12  6 11  7 10  8  9
>  Actual    scratch disk usage=   335802069 words.
> Erroneous write during file extend. write 61632511
> instead of 4096
> Probably out of disk space.
> and the calculation stops. I change %mem, %Maxdisk and
> test with direct procedure, but the problem continues.
> What can I do in this case?
> Thanks
> Rachel
>
>
> 		
> __________________________________
> Do you Yahoo!?
> Take Yahoo! Mail with you! Get it on your mobile phone.
> http://mobile.yahoo.com/maildemo
>
>
> -= This is automatically added to each message by the mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject:
> line and send your message to:  CHEMISTRY..at..ccl.net
>
> Send your subscription/unsubscription requests to:
> CHEMISTRY-REQUEST..at..ccl.net  HOME Page: http://www.ccl.net   | Jobs Page:
> http://www.ccl.net/jobs
>
> If your mail is bouncing from CCL.NET domain send it to the maintainer:
> Jan Labanowski,  jlabanow..at..nd.edu (read about it on CCL Home Page)
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>
>
>
>
>






From chemistry-request@ccl.net Thu Oct 28 04:52:28 2004
Received: from probity.mcc.ac.uk (probity.mcc.ac.uk [130.88.200.94])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9S9qQpH003462
	for <chemistry<<at>>ccl.net>; Thu, 28 Oct 2004 04:52:27 -0500
Received: from tcc02.ch.man.ac.uk ([130.88.83.2] helo=TCC02)
	by probity.mcc.ac.uk with smtp (Exim 4.20)
	id 1CN79V-000LWX-Al
	for chemistry=at=ccl.net; Thu, 28 Oct 2004 11:05:05 +0100
Message-ID: <001801c4bcd5$0e40cc00$02535882@TCC02>
Reply-To: "Mahesh" <mahesh.sundararajan=at=student.manchester.ac.uk>
From: "Mahesh" <mahesh.sundararajan=at=student.manchester.ac.uk>
To: <chemistry=at=ccl.net>
Subject: Amber Paramters for Nickel
Date: Thu, 28 Oct 2004 11:01:12 +0100
MIME-Version: 1.0
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_0015_01C4BCDD.6FC740A0"
X-Priority: 3
X-MSMail-Priority: Normal
X-Mailer: Microsoft Outlook Express 6.00.2900.2180
X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180
X-Scanner: exiscan for exim4 (http://duncanthrax.net/exiscan/) *1CN79V-000LWX-Al*J57Hdm2Fq4o*
X-Spam-Status: No, hits=1.0 required=7.5 tests=HTML_50_60,HTML_MESSAGE 
	autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net

This is a multi-part message in MIME format.

------=_NextPart_000_0015_01C4BCDD.6FC740A0
Content-Type: text/plain;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Dear All:

I want to do some QM/MM calculation on Nickel enzymes.

Is there any MM parameters available for Nickel?. I checked in the =
literature,
I can't find any!!.=20

Thanks in adavnce,

Regards,
Mahesh S
------=_NextPart_000_0015_01C4BCDD.6FC740A0
Content-Type: text/html;
	charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.2900.2523" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear All:</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I want to do some QM/MM calculation on =
Nickel=20
enzymes.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Is there any&nbsp;MM parameters =
available for=20
Nickel?. I checked in the literature,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>I can't find any!!. </FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Thanks in adavnce,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Mahesh S</FONT></DIV></BODY></HTML>

------=_NextPart_000_0015_01C4BCDD.6FC740A0--



From chemistry-request@ccl.net Thu Oct 28 10:25:49 2004
Received: from hispania.ti.uam.es (hispania.ti.uam.es [150.244.9.54])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9SFPlEB022618
	for <CHEMISTRY(at)ccl.net>; Thu, 28 Oct 2004 10:25:48 -0500
Received: from obelix.ti.uam.es (obelix.ti.uam.es [150.244.9.46])
	by hispania.ti.uam.es (8.9.3/8.9.3/UAM) with ESMTP id RAA19389
	for <CHEMISTRY(at)ccl.net>; Thu, 28 Oct 2004 17:38:28 +0200 (MEST)
Received: from uam-94b9880xr5r.uam.es (victor.qfa.uam.es [150.244.120.18])by
	 obelix.ti.uam.es (8.12.11/8.11.3/UAM) with ESMTP id i9SFcIf5012363for 
	<CHEMISTRY(at)ccl.net>; Thu, 28 Oct 2004 17:38:23 +0200
Message-Id: <6.0.0.22.1.20041028173533.019f2320(at)pop.uam.es>
X-Sender: vferro(at)pop.uam.es
X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22
Date: Thu, 28 Oct 2004 17:38:22 +0200
To: CHEMISTRY(at)ccl.net
From: Victor Ferro <victor.ferro(at)uam.es>
Subject: Localized orbitals in HyperChem???
Mime-Version: 1.0
Content-Type: text/plain;
	charset=us-ascii;
	format=flowed
X-imss-version: 2.7
X-imss-result: Passed
X-imss-approveListMatch: *@uam.es
X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net

Hi:

Is it possible to calculate and to represent localized molecular orbitals 
using the HyperChem programm package (We have the version 5.11).

Thanks a lot


Victor



From chemistry-request@ccl.net Thu Oct 28 16:32:59 2004
Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9SLWwkv023644
	for <chemistry..at..ccl.net>; Thu, 28 Oct 2004 16:32:58 -0500
Received: from frenkel.ps.uci.edu (frenkel.ps.uci.edu [128.200.11.119])
	by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i9SLjWsI023712
	for <chemistry..at..ccl.net>; Thu, 28 Oct 2004 14:45:33 -0700
Content-Type: text/plain;
  charset="us-ascii"
From: wei <wzhuang..at..uci.edu>
Reply-To: wzhuang..at..uci.edu
Organization: university of california at Irvine
To: chemistry..at..ccl.net
Subject: looking for a specific kind of proteins
Date: Thu, 28 Oct 2004 14:39:53 -0400
User-Agent: KMail/1.4.1
MIME-Version: 1.0
Message-Id: <200410281439.54012.wzhuang..at..uci.edu>
X-NACS_ES-MailScanner: No viruses found
X-Spam-Status: No, hits=0.7 required=7.5 tests=DATE_IN_PAST_03_06 
	autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9SLWxkv023650

Dear All:

I am looking for a protein which can be used for the testing of my new simulation methodology. This protein needs to have a size smaller than 70 residues,several well defined secondary structure regions, it should be stable in water under room temperature and pressure. it should have several controversial folding pathways, each of them should be well defined ( the configuration models (coordinate files) of intermediate states can be found in the references).

the size limit is not so strict, a larger size ( up to 300) will be ok.

Thanks for the suggestion. 



From chemistry-request@ccl.net Thu Oct 28 14:48:28 2004
Received: from mail.vu.nl (mail.vu.nl [130.37.129.161])
	by server.ccl.net (8.12.8/8.12.8) with ESMTP id i9SJmREB014066
	for <CHEMISTRY..at..ccl.net>; Thu, 28 Oct 2004 14:48:27 -0500
Received: from few.vu.nl (126-243.vu.surfnetthuis.nl [145.98.126.243])
	by mail.vu.nl (8.11.6/8.11.6) with ESMTP id i9SJxeQ29232;
	Thu, 28 Oct 2004 21:59:40 +0200
Date: Thu, 28 Oct 2004 22:03:18 +0200
Subject: Re: CCL:predicting circular dichroism spectra
Content-Type: text/plain; charset=WINDOWS-1252; format=flowed
Mime-Version: 1.0 (Apple Message framework v553)
Cc: CHEMISTRY..at..ccl.net
To: avw1557..at..ksu.edu
From: Marcel Swart <m.swart..at..few.vu.nl>
In-Reply-To: <OFA72649F4.7EACC721-ONC1256F3B.0035D322-C1256F3B.0035F9B4..at..emea.givaudan.com>
Message-Id: <6961CA42-291C-11D9-82FF-000393AEC93C..at..few.vu.nl>
X-Mailer: Apple Mail (2.553)
X-MailScanner-Information: Please contact servicedesk..at..it.vu.nl for more information
X-MailScanner: Found to be clean
X-MailScanner-SpamCheck: geen spam, spamfilter (score=-4.9, vereist 5,
	BAYES_00 -4.90)
X-Spam-Status: No, hits=1.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR 
	autolearn=no version=2.61
X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on 
	servernd.ccl.net
Content-Transfer-Encoding: 8bit
X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i9SJmSEB014070

You could try ADF, that has this option implemented recently.
See: http://www.scm.com for more information on the program,
its utilities and how to obtain a trial license.

On Thursday, Oct 28, 2004, at 11:49 Europe/Amsterdam, 
andras.borosy..at..givaudan.com wrote:

> Hello all,
>
> I have recently begun working with salen type compounds and would like
> to run calculations to predict UV/CD spectra to compare to the
> experimental data.  Does anyone have experience with commercially
> available software (e.g. gaussian 03) and could recommend a good
> software package to use, and if possible what would be the best
> software package to use.  We are looking to purchase one.
>
> Thanks
>
> Alex Wiznycia
> Department of Chemistry
> Kansas State University
> 111 Willard Hall
> Manhattan KS 66506-3701
> email : avw1557..at..ksu.edu
                                            
dr. Marcel Swart

Theoretische Chemie
Vrije Universiteit Amsterdam
Faculteit der Exacte Wetenschappen

De Boelelaan 1083
1081 HV Amsterdam
The Netherlands

Tel      +31-20-4447619
Fax      +31-20-4447629
E-mail   m.swart..at..few.vu.nl
Web      http://www.few.vu.nl/~swart
                                            




