From chemistry-request@ccl.net Tue Apr 26 17:27:16 2005 Received: from web30611.mail.mud.yahoo.com (web30611.mail.mud.yahoo.com [68.142.201.244]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3QLR9gL005036 for ; Tue, 26 Apr 2005 17:27:09 -0400 Received: (qmail 19766 invoked by uid 60001); 26 Apr 2005 20:27:08 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=CdH9wYrlM5GJXyR83Kkl6Z267LkVKUknw0b3ScOvUf8qsNatxbH26jgC60IUfMwKVuyNHRbwexgUwDTq/09D3f0+bh/T3S46BNJzevQFk0jlH/MXhsSOVqTDbhjw4d6koCyMF9kIsJShel8Hpi1TZulymrroQ+hNQFZt4aoquEE= ; Message-ID: <20050426202708.19764.qmail !v! web30611.mail.mud.yahoo.com> Received: from [81.181.225.33] by web30611.mail.mud.yahoo.com via HTTP; Tue, 26 Apr 2005 15:27:08 CDT Date: Tue, 26 Apr 2005 15:27:08 -0500 (CDT) From: Joaquin Barroso Flores Subject: Re: CCL:W:carbon nanotube with cap geometry To: David Gallagher , "Hector, Ismail" , chemistry !v! ccl.net In-Reply-To: 6667 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1346079561-1114547228=:19352" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=3.1 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_YAHOO_RCVD,HTML_20_30,HTML_MESSAGE autolearn=no version=3.0.1 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-1346079561-1114547228=:19352 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Try searchin for the software created by Mircea Diudea at Romania (Babes Bolyai University) for the construction of nanotubes and buckys, U only have to tell it haw many atoms and perhaps which point group!!!!! its great!!!! but the problem is i dont know if they have a freeware version best wishes David Gallagher wrote: H56 Hect63r, I have a C460 with both ends closed, as CAChe or pdb format. Let me know which you want and can email it to you. Regards David Gallagher At 10:36 AM 4/23/2005, Hector, , Ismail wrote: >Hi CCL.net, > > Would anyone have the cartesian coordinates or z-matrix for any > carbon nanotube (of any length or chirality) with an endcap on it? I > tried searching the web for one, but I could only find open-ended ones. > >Thanks, >Hector > > > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST !v! ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >use the Web based form from CCL Home Page -= 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 !v! ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST !v! ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ********************************************************** Q. Joaqumn Barroso Flores Instituto de Qummica UNAM Correo Alterno: joaquin_barroso !v! correo.unam.mx ********************************************************** --------------------------------- Do You Yahoo!? Yahoo! Net: La mejor conexisn a internet y 25MB extra a tu correo por $100 al mes. --0-1346079561-1114547228=:19352 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Try searchin for the software created by Mircea Diudea at Romania (Babes Bolyai University) for the construction of nanotubes and buckys, U only have to tell it haw many atoms and perhaps which point group!!!!! its great!!!! but the problem is i dont know if they have a freeware version

best wishes

David Gallagher <dgallagher !v! cachesoftware.com> wrote:

H56 Hect63r,

I have a C460 with both ends closed, as CAChe or pdb format. Let me know
which you want and can email it to you.

Regards
David Gallagher

At 10:36 AM 4/23/2005, Hector, , Ismail wrote:
>Hi CCL.net,
>
> Would anyone have the cartesian coordinates or z-matrix for any
> carbon nanotube (of any length or chirality) with an endcap on it? I
> tried searching the web for one, but I could only find open-ended ones.
>
>Thanks,
>Hector
>
>
>
>Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST !v! ccl.net
>HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs
>
>use the Web based form from CCL Home Page

-= 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 !v! ccl.net

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use the Web based form from CCL Home Page
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

**********************************************************
Q. Joaqumn Barroso Flores

Instituto de Qummica UNAM
Correo Alterno: joaquin_barroso !v! correo.unam.mx
**********************************************************

Do You Yahoo!?
Yahoo! Net: La mejor conexisn a internet y 25MB extra a tu correo por $100 al mes.
--0-1346079561-1114547228=:19352-- From chemistry-request@ccl.net Wed Apr 27 03:24:05 2005 Received: from web26806.mail.ukl.yahoo.com (web26806.mail.ukl.yahoo.com [217.146.176.82]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3R7Nig1001081 for ; Wed, 27 Apr 2005 03:23:52 -0400 Received: (qmail 51634 invoked by uid 60001); 27 Apr 2005 07:23:36 -0000 Message-ID: <20050427072336.51632.qmail !v! web26806.mail.ukl.yahoo.com> Received: from [213.140.56.83] by web26806.mail.ukl.yahoo.com via HTTP; Wed, 27 Apr 2005 09:23:36 CEST Date: Wed, 27 Apr 2005 09:23:36 +0200 (CEST) From: may abdelghani Subject: YES ...Viewing IRC calculation To: Paul Momoh Cc: ccl In-Reply-To: 6667 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1573198481-1114586616=:50832" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_40_50,HTML_MESSAGE autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-1573198481-1114586616=:50832 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hello, yes he can ..." the program reads the vibrational frequencies and intensities directly from Gaussian 98/03, Hyeprchem, ADFand ZINDO or "free-format" files and produces vibrational spectra of molecules in the ASCII data format. " there is also "ALP-vibro" which is a program for visualization/animation of molecular vibrations computed by Gaussian 98 (http://www.sg-chem.net/alp-vibro/) Paul Momoh wrote: Thanks May, Can SWizard read directly from *.out or *.log files without my having to copy/paste coordinates? On 4/26/05, may abdelghani wrote: > Hello, > swizard (http://www.sg-chem.net/swizard/) ... can do it > > ________________________________ > Dicouvrez le nouveau Yahoo! Mail : 250 Mo d'espace de stockage pour vos > mails ! > Criez votre Yahoo! Mail > > --------------------------------- Dicouvrez le nouveau Yahoo! Mail : 250 Mo d'espace de stockage pour vos mails ! Criez votre Yahoo! Mail --0-1573198481-1114586616=:50832 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Hello,

yes he can ..." the program reads the vibrational frequencies and intensities directly from Gaussian 98/03, Hyeprchem, ADFand ZINDO or "free-format" files and produces vibrational spectra of molecules in the ASCII data format. "

there is also "ALP-vibro" which is a program for visualization/animation of molecular vibrations computed by Gaussian 98 (http://www.sg-chem.net/alp-vibro/)
Paul Momoh <momohpaul !v! gmail.com> wrote:

Thanks May,
Can SWizard read directly from *.out or *.log files without my having
to copy/paste coordinates?

On 4/26/05, may abdelghani wrote:
> Hello,
> swizard (http://www.sg-chem.net/swizard/) ... can do it
>
> ________________________________
> Dicouvrez le nouveau Yahoo! Mail : 250 Mo d'espace de stockage pour vos
> mails !
> Criez votre Yahoo! Mail
>
>

Dicouvrez le nouveau Yahoo! Mail : 250 Mo d'espace de stockage pour vos mails !
Criez votre Yahoo! Mail --0-1573198481-1114586616=:50832-- From chemistry-request@ccl.net Wed Apr 27 11:16:29 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3RFGSkW022368 for ; Wed, 27 Apr 2005 11:16:28 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j3RFGSNr022367 for chemistry !=! ccl.net; Wed, 27 Apr 2005 11:16:28 -0400 Date: Wed, 27 Apr 2005 11:16:28 -0400 Message-Id: <200504271516.j3RFGSNr022367 !=! server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request !=! ccl.net using -f From: "Zhe, , Li" To: chemistry !=! ccl.net X-Web-Message-Number: 050427111226-22226 Subject: W:CAS Optimization Using Guassian Programm X-Spam-Status: No, score=-0.6 required=5.0 tests=ALL_TRUSTED, FORGED_YAHOO_RCVD autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear all: I have a question about CAS(12,10) optimization on benzamide. First, should I have to add the key word 'FullDiag' after the CAS? Second, if I add the key word, does it need so much memory that it is impossible to carry out the work on personal computer? Third, if anyone has some better advise, please contact me by E-mail: yihongzhurenlizhe !=! yahoo.com Thank you very much. a freshman on computational chemistry Zhe Li From chemistry-request@ccl.net Tue Apr 26 22:43:55 2005 Received: from web53402.mail.yahoo.com (web53402.mail.yahoo.com [206.190.37.49]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3R2hoKJ019263 for ; Tue, 26 Apr 2005 22:43:50 -0400 Received: (qmail 43085 invoked by uid 60001); 27 Apr 2005 02:43:49 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=BmvL8nHCuRdxbzdxKF11YdrwjIkWRsJvMxlGQbxvOd+6PUY/OfZHehdYN/A1//iUQw3FPTdaaRhUVlmf1TLyXJNkQ9hdARnu3xjwFVL/L4S0299AG2eniBuRQn8zPh6GG6tqddBxEhhsshcCNL4A33i5Qt22dZDPZD+SnOFSU8A= ; Message-ID: <20050427024349.43083.qmail !=! web53402.mail.yahoo.com> Received: from [24.193.244.184] by web53402.mail.yahoo.com via HTTP; Tue, 26 Apr 2005 19:43:49 PDT Date: Tue, 26 Apr 2005 19:43:49 -0700 (PDT) From: Vani Krishna Subject: Matching classical & abinitio normal modes To: chemistry MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=0.9 required=5.0 tests=DNS_FROM_RFC_ABUSE, FROM_ENDS_IN_NUMS autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hello: I have a question regarding the matching of normal modes for optimizations to determine the intra bond force constants. How to resolve a one to many mapping between the two? Some of the classical frequencies match more than one abinitio ferquencies, and some are not matched at all. Ofcourse i hope that during the optimization process this matching might improve, but I want to make sure that iam doing the most appropriate matching. And also should every frequency be matched? also what kind of scaling of frequencies is used for HF and DFT before comparing them with classical frequencies? Any references would be great. Iam new to force-field development and this would help me a lot. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From chemistry-request@ccl.net Tue Apr 26 17:44:31 2005 Received: from web30607.mail.mud.yahoo.com (web30607.mail.mud.yahoo.com [68.142.200.130]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j3QLiPr6006258 for ; Tue, 26 Apr 2005 17:44:25 -0400 Received: (qmail 99781 invoked by uid 60001); 26 Apr 2005 20:44:24 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=JrmENmhLfv+H8ysmDkEmwNhyePyUpDZCH5oMuThSNV79itOZeCy9ALZhEHNtbI26tbhutRFReJEZ4Q7tvpXlGDOQShhcAbeuW+H0wttRwI+C+OYLZHL62dUt0JGRBt+E57uEYRYbYEvxILeiQqIa6Vv9/EYIJSmPsfTO3e+WKfo= ; Message-ID: <20050426204424.99779.qmail !v! web30607.mail.mud.yahoo.com> Received: from [81.181.225.33] by web30607.mail.mud.yahoo.com via HTTP; Tue, 26 Apr 2005 15:44:24 CDT Date: Tue, 26 Apr 2005 15:44:24 -0500 (CDT) From: Joaquin Barroso Flores Subject: Re: CCL:NBO bond analysis To: Marius Retegan , chemistry !v! ccl.net In-Reply-To: 6667 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1372362376-1114548264=:98966" Content-Transfer-Encoding: 8bit X-Spam-Status: No, score=3.1 required=5.0 tests=DNS_FROM_RFC_ABUSE, FORGED_YAHOO_RCVD,HTML_20_30,HTML_MESSAGE autolearn=no version=3.0.1 X-Spam-Level: *** X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net --0-1372362376-1114548264=:98966 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Probably you should also include RESONANCE at the NBO keywords since it seems delocalization is a great issue in your molecule. Chek the percent of electronic density in the Non Lewis Basis so you know if u'r getting a good Lewis description of the electronic density, if this is too high then try to use the above keyword Best wishes s Retegan wrote: Hello to all This is my first request so I hope I won't sound stupid. I try to do a NBO analisis on (CO)5W-SbPh2Cl in Gaussian 03. This is the input #p rb3lyp/genecp iop(6/7=3) pop=full pop=nboread gfinput gfprint 5d 7f >. >. $nbo plot file=outnbo $end I used lanl2dz+polarization as basis set for Sb and W, and the corresponding ECP. For the others elements 6-311g(d,p). The problem: From the 5 CO groups, only 3 have bound orbitals with W, the other 2 are separate molecular units. Is this normal? If not any idea how to fix this? If additional info is required pleas send me an e-mail. Thank you -= 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 !v! ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST !v! ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your is mail bouncing from ccl.net domain due to spam filters, please use the Web based form from CCL Home Page -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ********************************************************** Q. Joaqumn Barroso Flores Instituto de Qummica UNAM Correo Alterno: joaquin_barroso !v! correo.unam.mx ********************************************************** --------------------------------- Do You Yahoo!? Yahoo! Net: La mejor conexisn a internet y 25MB extra a tu correo por $100 al mes. --0-1372362376-1114548264=:98966 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit

Probably you should also include RESONANCE at the NBO keywords since it seems delocalization is a great issue in your molecule. Chek the percent of electronic density in the Non Lewis Basis so you know if u'r getting a good Lewis description of the electronic density, if this is too high then try to use the above keyword

Best wishes

s Retegan <retegan.marius !v! gmail.com> wrote:

Hello to all
This is my first request so I hope I won't sound stupid.
I try to do a NBO analisis on (CO)5W-SbPh2Cl in Gaussian 03.
This is the input
#p rb3lyp/genecp iop(6/7=3) pop=full pop=nboread gfinput gfprint 5d 7f
>.
>.
$nbo plot file=outnbo $end
I used lanl2dz+polarization as basis set for Sb and W, and the
corresponding ECP. For the others elements 6-311g(d,p).
The problem: From the 5 CO groups, only 3 have bound orbitals with W,
the other 2 are separate molecular units.
Is this normal? If not any idea how to fix this?
If additional info is required pleas send me an e-mail.
Thank you

-= This is automatically added to each message by the mailing script =-
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--0-1372362376-1114548264=:98966-- From chemistry-request@ccl.net Tue Apr 26 16:10:38 2005 Received: from mail.mdli.com (mail.mdli.com [208.200.221.8]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3QKAXeO000304 for ; Tue, 26 Apr 2005 16:10:34 -0400 Received: from exch-sl02.mdli.com (exch-sl02.mdli.com [145.36.243.10]) by mail.mdli.com (Postfix) with ESMTP id 842FEB5E25 for ; Tue, 26 Apr 2005 11:10:09 -0700 (PDT) Received: by exch-sl02.mdli.com with Internet Mail Service (5.5.2657.72) id ; Tue, 26 Apr 2005 11:10:09 -0700 Message-ID: From: Terry Wright To: chemistry(at)ccl.net Subject: RE: Final Call for Papers: Public Information Databases: CINF Div ision - ACS Washington - Aug. 28-Sept 1. Date: Tue, 26 Apr 2005 11:10:07 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C54A8B.2D510398" X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE, HTML_NONELEMENT_30_40 autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C54A8B.2D510398 Content-Type: text/plain You and your colleagues are cordially invited to present a paper in the CINF symposium entitled: Public Information Databases at the ACS meeting in Washington D.C., August 18 Sept 1 Summary Although the value of commercial chemistry and biology databases is well known and appreciated, there is also valuable considerable information in these areas that is in the public domain. In this session we invite speakers to discuss the various types and quality of public information databases in the area of chemistry, biology and related fields. Comparisons of these information sources and examples of their utility are especially encouraged. If you are interested, please submit an abstract for this session via the OASYS system under CINF. Please note the deadline is coming up soon, May 3. For your convenience, a link is provided below: http://oasys.acs.org/acs/230nm/cinf/papers/index.cgi Thank you for your interest. Terry Wright Terry Wright MDL Information Systems 14600 Catalina Street San Leandro, CA 94577 Phone: 510-357-2222 ext. 1392 Email: terryw(at)mdli.com Terry Wright MDL Information Systems 14600 Catalina Street San Leandro, CA 94577 Phone: 510-357-2222 ext. 1392 Email: terryw(at)mdli.com ------_=_NextPart_001_01C54A8B.2D510398 Content-Type: text/html

You and your colleagues are cordially invited to present a paper in the CINF symposium entitled: Public Information Databases at the ACS meeting in Washington D.C., August 18 Sept 1

Summary

Although the value of commercial chemistry and biology databases is well known and appreciated, there is also valuable considerable information in these areas that is in the public domain.

In this session we invite speakers to discuss the various types and quality of public information databases in the area of chemistry, biology and related fields. Comparisons of these information sources and examples of their utility are especially encouraged.

If you are interested, please submit an abstract for this session via the OASYS system under CINF.

Please note the deadline is coming up soon, May 3.

For your convenience, a link is provided below:

http://oasys.acs.org/acs/230nm/cinf/papers/index.cgi

Thank you for your interest.

Terry Wright

MDL Information Systems

14600 Catalina Street

San Leandro, CA 94577

Phone: 510-357-2222 ext. 1392

Email: terryw(at)mdli.com

Terry Wright

MDL Information Systems

14600 Catalina Street

San Leandro, CA 94577

Phone: 510-357-2222 ext. 1392

Email: terryw(at)mdli.com

------_=_NextPart_001_01C54A8B.2D510398-- From chemistry-request@ccl.net Tue Apr 26 19:48:41 2005 Received: from turmiel.ch.uj.edu.pl (turmiel.ch.uj.edu.pl [149.156.71.252]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3QNmZTW011887 for ; Tue, 26 Apr 2005 19:48:36 -0400 Received: from turmiel.ch.uj.edu.pl (localhost.localdomain [127.0.0.1]) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8) with ESMTP id j3QNmUb1013082 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NO); Wed, 27 Apr 2005 01:48:30 +0200 From: zborowsk*at*chemia.uj.edu.pl Received: (from apache@localhost) by turmiel.ch.uj.edu.pl (8.12.8/8.12.8/Submit) id j3QNmTEO013080; Wed, 27 Apr 2005 01:48:29 +0200 X-Authentication-Warning: turmiel.ch.uj.edu.pl: apache set sender to zborowsk*at*chemia.uj.edu.pl using -f Received: from 213.134.172.104 (SquirrelMail authenticated user zborowsk) by mail.ch.uj.edu.pl with HTTP; Wed, 27 Apr 2005 01:48:29 +0200 (CEST) Message-ID: <1417.213.134.172.104.1114559309.squirrel*at*mail.ch.uj.edu.pl> Date: Wed, 27 Apr 2005 01:48:29 +0200 (CEST) Subject: Re: CCL:coordinates output To: In-Reply-To: <426D0F37.4030008*at*ahpcrc.org> References: <426D0F37.4030008*at*ahpcrc.org> X-Priority: 3 Importance: Normal Cc: X-Mailer: SquirrelMail (version 1.2.11) MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-2 Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Hi I am not sure what you really want to do Gaussian prints coordinate after every step For example, they can be displayed by the Molden program Do you want to create the file with optimized structures on the relaxed PES only? If yes (and if you use Linux/Unix, not Windows) I have an script in awk written by my friend and I can send it to you Best regards > Hi all, > > Could you advise me how to get a coordinate set (cartesian or Z-matrix) > for a relaxed PES scan? > Gaussian 98 prints optimized parameters after a stationary point is > found, but I want to extract an optimized structure at each point. > > Thanks, > > Genzo > Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk*at*chemia.uj.edu.pl ICQ 158385743 gg 3817259 From chemistry-request@ccl.net Wed Apr 27 12:50:14 2005 Received: from mail.interware.hu (mail.interware.hu [195.70.32.130]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3RGo876029845 for ; Wed, 27 Apr 2005 12:50:08 -0400 Received: from caracas-2703.adsl.interware.hu ([213.178.110.143] helo=cthulhu) by mail.interware.hu with smtp (Exim 4.50 #1 (Debian)) id 1DQpjh-0006JT-Et; Wed, 27 Apr 2005 18:50:05 +0200 Message-ID: <003401c54b51$fc5c78c0$6401a8c0@cthulhu> From: "Tamas E. Gunda" To: , References: <426D0F37.4030008 *o* ahpcrc.org> <1417.213.134.172.104.1114559309.squirrel *o* mail.ch.uj.edu.pl> Subject: Re: CCL:coordinates output Date: Wed, 27 Apr 2005 18:53:03 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1478 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1478 X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id j3RGoE76029868 Mol2Mol can input gaussian output files in browse mode, thus you can display and/or save all embedded molecules marked with "standard orientation" http://web.interware.hu/frenzy/mol2mol/index.html Dr. Tamas E. Gunda Dept. of Pharmaceutical Chemistry University of Debrecen POBox 36 H-4010 Debrecen, Hungary tgunda (AT) puma.unideb.hu ----- Original Message ----- From: To: Cc: Sent: Wednesday, April 27, 2005 0:48 AM Subject: CCL:coordinates output > Hi > I am not sure what you really want to do > > Gaussian prints coordinate after every step > For example, they can be displayed by the Molden program > > Do you want to create the file with optimized structures on the relaxed > PES only? > > If yes (and if you use Linux/Unix, not Windows) I have an script in awk > written by my friend and I can send it to you > > Best regards > > > Hi all, > > > > Could you advise me how to get a coordinate set (cartesian or Z-matrix) > > for a relaxed PES scan? > > Gaussian 98 prints optimized parameters after a stationary point is > > found, but I want to extract an optimized structure at each point. > > > > Thanks, > > > > Genzo > > > > > > > Krzysztof Zborowski > Faculty of Chemistry > Jagiellonian University > 3 Ingardena Street > 30-060 Krakow > Poland > phone: +48(12)632-4888 ext. 2064 or 2067 > fax: +48(12)634-05-15 > email: zborowsk *o* chemia.uj.edu.pl > ICQ 158385743 > gg 3817259 > > > From chemistry-request@ccl.net Wed Apr 27 11:41:55 2005 Received: from relay4.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j3RFfnmf024365 for ; Wed, 27 Apr 2005 11:41:50 -0400 X-Envelope-To: gamess #%# lists.ciw.edu Received: from [192.168.5.1] (CPE0050bfacfe11-CM00122573bb18.cpe.net.cable.rogers.com [24.42.82.45]) (authenticated bits=0) by sycorax.delfa.net (8.13.3/8.13.3/Sycorax.Delfa) with ESMTP id j3REh5G6019995 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NO); Wed, 27 Apr 2005 18:43:07 +0400 Message-ID: <426FA4F8.4000805 #%# xenon.spb.ru> Date: Wed, 27 Apr 2005 10:43:04 -0400 From: Dmitri Rozmanov User-Agent: Debian Thunderbird 1.0 (X11/20050116) X-Accept-Language: en-us, en MIME-Version: 1.0 To: CCL , GAMESS Subject: rhf water with GAMESS Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.2 required=5.0 tests=UPPERCASE_25_50 autolearn=no version=3.0.1 X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on server.ccl.net Dear Colleagues, I am trying to do some testing calculation of the water molecule with GAMESS by RHF method. What is strange that GAMESS from 19 MAY 2004 (R3) gives me different frequencies than GAMESS from 14 JAN 2003 (R2) using exactly the same input file: Here is what I get for the located point using 19 MAY 2004 (R3) version: TOTAL ENERGY = -76.0468293144 1 2 3 4 5 FREQUENCY: 280.21 236.50 193.39 0.00 0.01 REDUCED MASS: 1.04398 1.00783 1.12583 6.00352 6.00351 IR INTENSITY: 2.76026 0.00000 7.96375 0.00000 0.00000 6 7 8 9 FREQUENCY: 0.02 1748.03 4157.15 4280.38 REDUCED MASS: 6.00530 1.08292 1.04494 1.08395 IR INTENSITY: 0.00000 2.00034 1.13027 2.55149 Here is what I get for the located point using 14 JAN 2003 (R2) version: TOTAL ENERGY = -76.0468293144 1 2 3 4 5 FREQUENCY: 0.04 0.04 0.04 0.63 0.67 REDUCED MASS: 6.00352 5.98077 5.99453 1.00823 1.04374 IR INTENSITY: 0.00000 0.00001 0.00000 0.03196 2.73975 6 7 8 9 FREQUENCY: 0.73 1753.77 4166.99 4290.52 REDUCED MASS: 1.12669 1.08346 1.04444 1.08404 IR INTENSITY: 8.41034 2.67853 0.48998 1.76857 Does anybody know what is going on? Below, the input itself is given. Thank you in advance. Regards, --- Dmitri Rozmanov. ----------------------------------------------------------------------------------- $CONTRL SCFTYP=RHF ICHARG=0 MULT=1 RUNTYP=OPTIMIZE EXETYP=RUN MAXIT=200 COORD=UNIQUE $END $SYSTEM TIMLIM=30000 MEMORY=15000000 $END $BASIS GBASIS=DZV NDFUNC=1 NPFUNC=1 DIFFSP=.F. DIFFS=.F. $END $SCF CONV=1.0d-8 DIRSCF=.TRUE. $END $STATPT OPTTOL = 1e-10 NSTEP=300 HSSEND=.TRUE. $END $GUESS GUESS=HUCKEL !GUESS=MOREAD $END $FORCE TEMP(1)=298.15 !NVIB=2 $END $DATA H2O RHF DZV(1p1d) OPTIMIZE/HESSIAN / R-1080-01 C1 O 8.0 0.0 0.0 0.0 H 1.0 0.0 0.7 0.7 H 1.0 0.0 0.7 -0.7 $END