From owner-chemistry@ccl.net Mon Nov 25 09:58:00 2013 From: "Andrew Yeung andrew.yeung|,|chem.tamu.edu" To: CCL Subject: CCL:G: PES of a triatomic molecule Message-Id: <-49373-131125095634-9500-ZkZTTAfac8oaXdazT+2/yg/a\server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 25 Nov 2013 08:56:29 -0600 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung*o*chem.tamu.edu] You can't use opt(cart) and opt(modredundant) at the same time. How about defining the molecule with a Z-matrix? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 Fax: 979 845 0158 On 2013-11-24 11:08 AM, Jorge jorge.m.seminario%a%gmail.com wrote: > Sent to CCL by: Jorge [jorge.m.seminario_+_gmail.com] > Try > Opt=Cartesian > Regards > Jorge > > Sent from my iPhone > >> On Nov 23, 2013, at 4:54 PM, "mike Andaham mymagnussen],[hotmail.com" wrote: >> >> >> Sent to CCL by: "mike Andaham" [mymagnussen a hotmail.com] >> Hi all, >> >> I am quite new to Gaussian and I encountered a problem. I am trying to run a PES of the C-C-Cl molecule. The problem is that this molecule has a 2Sigma and 2PI states almost isoenergetic and, in fact, the 2PI splits into two components, one with a 2A' symmetry that should interact with the 2A' (from the 2sigma). >> >> I am able to obtain the two minimum (one is linear the other bent) but when I run a PES scan (with the opt=modredundant) it stops with an error when it reaches the 180 degrees (with a linear error). This is one of the most important parts, I wonder if there any way of doing the PES including the 180 degrees? (so far I can do it from 120 to 178 degrees). I tried opt=z-matrix, opt=modredundant, sc=qf, with symmetry, no symmetry.... by the way, I am scanning the angle and the C-C bond leaving the C-Cl to optimize. >> >> Additionally, how can I get the correct symmetry of the PI upon splitting? (renner-teller effect). If I could get one I think that the other is simply using the guess=alter, but I can not get any symmetry for this state (it gives some unknown symmetry orbitals). >> >> Thanks, >> >> Mike> > From owner-chemistry@ccl.net Mon Nov 25 11:52:00 2013 From: "Stephen.Garrison:srnl.doe.gov" To: CCL Subject: CCL:G: PES of a triatomic molecule Message-Id: <-49374-131125114505-23676-FTT/jzTaM4V1Jhu/A8Neyw|a|server.ccl.net> X-Original-From: Stephen.Garrison]_[srnl.doe.gov Content-Type: multipart/alternative; boundary="=_alternative 005BF7A085257C2E_=" Date: Mon, 25 Nov 2013 11:44:31 -0500 MIME-Version: 1.0 Sent to CCL by: Stephen.Garrison]-[srnl.doe.gov This is a multipart message in MIME format. --=_alternative 005BF7A085257C2E_= Content-Type: text/plain; charset="US-ASCII" One solution is to use a dummy variable (X) that has a fixed bond length (generally of 1) from the central carbon, a fixed C-C-X angle (generally 90 deg.) and a fixed C-C-X-Cl dihedral at 180 deg. Then you run a PES changing the Cl-C-X bond angle. Just make sure your PES scan runs with a Cl-C-X bond angle that is greater than 0 so that Cl-C-X are not co-linear. You probably also need to do guess=always or nosymm because Gaussian may get confused when the symmetry changes. Also, you might have better luck if you go from the high symmetry state to the lower symmetry state. Stephen -- Stephen L. Garrison, Ph.D. - H-Canyon Technical Support Engineering - Assistant Editor, Int'l. Journal of Hydrogen Energy Savannah River Site 704-2H, Room 190 Aiken, SC 29808 803-208-8523 Stephen.Garrison~!~SRNL.doe.gov > From: "Andrew Yeung andrew.yeung|,|chem.tamu.edu" To: "Garrison, Stephen " , Date: 11/25/2013 10:46 AM Subject: CCL:G: PES of a triatomic molecule Sent by: owner-chemistry+stephen.garrison==srnl.doe.gov~!~ccl.net Sent to CCL by: Andrew Yeung [andrew.yeung*o*chem.tamu.edu] You can't use opt(cart) and opt(modredundant) at the same time. How about defining the molecule with a Z-matrix? Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 Fax: 979 845 0158 On 2013-11-24 11:08 AM, Jorge jorge.m.seminario%a%gmail.com wrote: > Sent to CCL by: Jorge [jorge.m.seminario_+_gmail.com] > Try > Opt=Cartesian > Regards > Jorge > > Sent from my iPhone > >> On Nov 23, 2013, at 4:54 PM, "mike Andaham mymagnussen],[hotmail.com" wrote: >> >> >> Sent to CCL by: "mike Andaham" [mymagnussen a hotmail.com] >> Hi all, >> >> I am quite new to Gaussian and I encountered a problem. I am trying to run a PES of the C-C-Cl molecule. The problem is that this molecule has a 2Sigma and 2PI states almost isoenergetic and, in fact, the 2PI splits into two components, one with a 2A' symmetry that should interact with the 2A' (from the 2sigma). >> >> I am able to obtain the two minimum (one is linear the other bent) but when I run a PES scan (with the opt=modredundant) it stops with an error when it reaches the 180 degrees (with a linear error). This is one of the most important parts, I wonder if there any way of doing the PES including the 180 degrees? (so far I can do it from 120 to 178 degrees). I tried opt=z-matrix, opt=modredundant, sc=qf, with symmetry, no symmetry.... by the way, I am scanning the angle and the C-C bond leaving the C-Cl to optimize. >> >> Additionally, how can I get the correct symmetry of the PI upon splitting? (renner-teller effect). If I could get one I think that the other is simply using the guess=alter, but I can not get any symmetry for this state (it gives some unknown symmetry orbitals). >> >> Thanks, >> >> Mikehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 005BF7A085257C2E_= Content-Type: text/html; charset="US-ASCII" One solution is to use a dummy variable (X) that has a fixed bond length (generally of 1) from the central carbon, a fixed C-C-X angle (generally 90 deg.) and a fixed C-C-X-Cl dihedral at 180 deg.

Then you run a PES changing the Cl-C-X bond angle. Just make sure your PES scan runs with a Cl-C-X bond angle that is greater than 0 so that Cl-C-X are not co-linear.

You probably also need to do guess=always or nosymm because Gaussian may get confused when the symmetry changes.

Also, you might have better luck if you go from the high symmetry state to the lower symmetry state.

Stephen

--
Stephen L. Garrison, Ph.D.
 - H-Canyon Technical Support Engineering
- Assistant Editor, Int'l. Journal of Hydrogen Energy

Savannah River Site
704-2H, Room 190
Aiken, SC 29808
803-208-8523
Stephen.Garrison~!~SRNL.doe.gov



From:        "Andrew Yeung andrew.yeung|,|chem.tamu.edu" <owner-chemistry~!~ccl.net>
To:        "Garrison, Stephen " <stephen.garrison~!~srnl.doe.gov>,
Date:        11/25/2013 10:46 AM
Subject:        CCL:G: PES of a triatomic molecule
Sent by:        owner-chemistry+stephen.garrison==srnl.doe.gov~!~ccl.net




Sent to CCL by: Andrew Yeung [andrew.yeung*o*chem.tamu.edu]
You can't use opt(cart) and opt(modredundant) at the same time.

How about defining the molecule with a Z-matrix?

Andrew Yeung
Donald J. Darensbourg Research Group
Department of Chemistry, Texas A&M University
3255 TAMU
College Station, TX 77843-3255

Tel: 979 845 4837
Fax: 979 845 0158

On 2013-11-24 11:08 AM, Jorge jorge.m.seminario%a%gmail.com wrote:
> Sent to CCL by: Jorge [jorge.m.seminario_+_gmail.com]
> Try
> Opt=Cartesian
> Regards
> Jorge
>
> Sent from my iPhone
>
>> On Nov 23, 2013, at 4:54 PM, "mike Andaham mymagnussen],[hotmail.com" <owner-chemistry^_^ccl.net> wrote:
>>
>>
>> Sent to CCL by: "mike  Andaham" [mymagnussen a hotmail.com]
>> Hi all,
>>
>> I am quite new to Gaussian and I encountered a problem. I am trying to run a PES of the C-C-Cl molecule. The problem is that this molecule has a 2Sigma and 2PI states almost isoenergetic and, in fact, the 2PI splits into two components, one with a 2A' symmetry that should interact with the 2A' (from the 2sigma).
>>
>> I am able to obtain the two minimum (one is linear the other bent) but when I run a PES scan (with the opt=modredundant) it stops with an error when it reaches the 180 degrees (with a linear error). This is one of the most important parts, I wonder if there any way of doing the PES including the 180 degrees? (so far I can do it from 120 to 178 degrees). I tried opt=z-matrix, opt=modredundant, sc=qf, with symmetry, no symmetry.... by the way, I am scanning the angle and the C-C bond leaving the C-Cl to optimize.
>>
>> Additionally, how can I get the correct symmetry of the PI upon splitting? (renner-teller effect). If I could get one I think that the other is simply using the guess=alter, but I can not get any symmetry for this state (it gives some unknown symmetry orbitals).
>>
>> Thanks,
>>
>> Mike>
>


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--=_alternative 005BF7A085257C2E_=-- From owner-chemistry@ccl.net Mon Nov 25 14:05:00 2013 From: "zvitnik zvitnik[a]chem.bg.ac.rs" To: CCL Subject: CCL:G: PES of a triatomic molecule Message-Id: <-49375-131125110307-6950-wXyCtGP3xji3lkSM5J/xXA^-^server.ccl.net> X-Original-From: zvitnik Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Mon, 25 Nov 2013 17:02:56 +0100 MIME-Version: 1.0 Sent to CCL by: zvitnik [zvitnik()chem.bg.ac.rs] Did you try to turn your tri-atomic molecule in four-atomic by adding one Bq atom. If not, try to read: http://www.gaussian.com/g_tech/g_ur/m_molspec.htm Zeljko On 2013-11-23 23:54, mike Andaham mymagnussen],[hotmail.com wrote: > Sent to CCL by: "mike Andaham" [mymagnussen a hotmail.com] > Hi all, > > I am quite new to Gaussian and I encountered a problem. I am trying > to run a PES of the C-C-Cl molecule. The problem is that this > molecule > has a 2Sigma and 2PI states almost isoenergetic and, in fact, the 2PI > splits into two components, one with a 2A' symmetry that should > interact with the 2A' (from the 2sigma). > > I am able to obtain the two minimum (one is linear the other bent) > but when I run a PES scan (with the opt=modredundant) it stops with > an > error when it reaches the 180 degrees (with a linear error). This is > one of the most important parts, I wonder if there any way of doing > the PES including the 180 degrees? (so far I can do it from 120 to > 178 > degrees). I tried opt=z-matrix, opt=modredundant, sc=qf, with > symmetry, no symmetry.... by the way, I am scanning the angle and the > C-C bond leaving the C-Cl to optimize. > > Additionally, how can I get the correct symmetry of the PI upon > splitting? (renner-teller effect). If I could get one I think that > the > other is simply using the guess=alter, but I can not get any symmetry > for this state (it gives some unknown symmetry orbitals). > > Thanks, > > Mike > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ From owner-chemistry@ccl.net Mon Nov 25 15:38:00 2013 From: "Van Dam, Hubertus J HubertusJJ.vanDam|pnnl.gov" To: CCL Subject: CCL: API for the Basis Set Exchange Message-Id: <-49376-131125153524-20744-01WEz4bek1QV8m63gQ19tg*o*server.ccl.net> X-Original-From: "Van Dam, Hubertus J" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_FDD09CBD8676AE40957DCDAD24E9627A0191EC605FBBEMAIL04pnlg_" Date: Mon, 25 Nov 2013 12:35:03 -0800 MIME-Version: 1.0 Sent to CCL by: "Van Dam, Hubertus J" [HubertusJJ.vanDam-x-pnnl.gov] --_000_FDD09CBD8676AE40957DCDAD24E9627A0191EC605FBBEMAIL04pnlg_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Julien, The paper http://dx.doi.org/10.1021/ci600510j describes the implementation = of the Basis Set Exchange. In particular it refers to the Web Services inte= rface that should allow you to pull data from the exchange. The web service= s interface is described at http://purl.oclc.org/net/emsl/bse/services. If = you need help with this let me know. I have some requests from other people= as well and I need to find some time to address these queries. I am wonder= ing whether I should write a little tutorial on this topic. Huub van Dam Pacific Northwest National Laboratory Tel: 509-372-6441 > From: owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov]-[ccl.net [mailto:owner-c= hemistry+hubertus.vandam=3D=3Dpnnl.gov]-[ccl.net] On Behalf Of Julien Thibaul= t tchetchenko%gmail.com Sent: Saturday, November 23, 2013 1:46 PM To: Van Dam, Hubertus J Subject: CCL: API for the Basis Set Exchange Hi, I was wondering if anybody was aware of an open-source distribution of the = the basis set exchange database (https://bse.pnl.gov/bse/portal) so that pe= ople can install it locally and/or access the database through an API (REST= ? Java?) Regards, ~Julien -- Julien Thibault University of Utah Department of Biomedical Informatics Salt Lake City, UT --_000_FDD09CBD8676AE40957DCDAD24E9627A0191EC605FBBEMAIL04pnlg_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Julien= ,

 =

The paper http://dx.doi.org/10.1021/ci600510j describes the implem= entation of the Basis Set Exchange. In particular it refers to the Web Serv= ices interface that should allow you to pull data from the exchange. The we= b services interface is described at http://purl.oclc.org/net/emsl/bse/services. If you nee= d help with this let me know. I have some requests from other people as wel= l and I need to find some time to address these queries. I am wondering whe= ther I should write a little tutorial on this topic.

<= p class=3DMsoNormal style=3D'mso-margin-top-alt:auto;mso-margin-bottom-alt:= auto'>Huu= b van Dam
Pacific Northwest Nat= ional Laboratory
Tel:  509-372-6441



 

From: owner-chemistry+hu= bertus.vandam=3D=3Dpnnl.gov]-[ccl.net [mailto:owner-chemistry+hubertus.vandam= =3D=3Dpnnl.gov]-[ccl.net] On Behalf Of Julien Thibault tchetchenko%gma= il.com
Sent: Saturday, November 23, 2013 1:46 PM
To: Va= n Dam, Hubertus J
Subject: CCL: API for the Basis Set Exchange

 

Hi, 

I was wonder= ing if anybody was aware of an open-source distribution of the the basis se= t exchange database (https://bse= .pnl.gov/bse/portal) so that people can install it locally and/or acces= s the database through an API (REST? Java?)

Regards,

~Juli= en

 

--
Julien Thibault
University of Uta= h
Department of Biomedical Informatics
Salt Lake City, UT

= --_000_FDD09CBD8676AE40957DCDAD24E9627A0191EC605FBBEMAIL04pnlg_-- From owner-chemistry@ccl.net Mon Nov 25 16:26:01 2013 From: "Julien Thibault tchetchenko:+:gmail.com" To: CCL Subject: CCL: API for the Basis Set Exchange Message-Id: <-49377-131125162359-18686-MzPk3z0OIHCwaERTS/Lbxg]![server.ccl.net> X-Original-From: Julien Thibault Content-Type: multipart/alternative; boundary=e89a8ff24d9b1c131d04ec06fb5a Date: Mon, 25 Nov 2013 14:23:53 -0700 MIME-Version: 1.0 Sent to CCL by: Julien Thibault [tchetchenko*gmail.com] --e89a8ff24d9b1c131d04ec06fb5a Content-Type: text/plain; charset=ISO-8859-1 Thanks Huub, exactly what i was looking for... ~Julien 2013/11/25 Van Dam, Hubertus J HubertusJJ.vanDam|pnnl.gov < owner-chemistry[#]ccl.net> > Hi Julien, > > > > The paper http://dx.doi.org/10.1021/ci600510j describes the > implementation of the Basis Set Exchange. In particular it refers to the > Web Services interface that should allow you to pull data from the > exchange. The web services interface is described at > http://purl.oclc.org/net/emsl/bse/services. If you need help with this > let me know. I have some requests from other people as well and I need to > find some time to address these queries. I am wondering whether I should > write a little tutorial on this topic. > > *Huub van Dam* > Pacific Northwest National Laboratory > Tel: 509-372-6441 > > > > > > *From:* owner-chemistry+hubertus.vandam==pnnl.gov ~ ccl.net [mailto: > owner-chemistry+hubertus.vandam==pnnl.gov ~ ccl.net] *On Behalf Of *Julien > Thibault tchetchenko%gmail.com > *Sent:* Saturday, November 23, 2013 1:46 PM > *To:* Van Dam, Hubertus J > *Subject:* CCL: API for the Basis Set Exchange > > > > Hi, > > I was wondering if anybody was aware of an open-source distribution of the > the basis set exchange database (https://bse.pnl.gov/bse/portal) so that > people can install it locally and/or access the database through an API > (REST? Java?) > > Regards, > > ~Julien > > > > -- > Julien Thibault > University of Utah > Department of Biomedical Informatics > Salt Lake City, UT > -- Julien Thibault University of Utah Department of Biomedical Informatics Salt Lake City, UT --e89a8ff24d9b1c131d04ec06fb5a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks Huub, exactly what i was looking for...
~Julien=


2013/11/2= 5 Van Dam, Hubertus J HubertusJJ.vanDam|pnnl.go= v <owner-chemistry[#]ccl.net>

Hi Julien,=

=A0<= /p>

The paper http://dx.doi.org/10.= 1021/ci600510j describes the implementation of the Basis Set Exchange. = In particular it refers to the Web Services interface that should allow you= to pull data from the exchange. The web services interface is described at= h= ttp://purl.oclc.org/net/emsl/bse/services. If you need help with this l= et me know. I have some requests from other people as well and I need to fi= nd some time to address these queries. I am wondering whether I should writ= e a little tutorial on this topic.

Huub van Dam=
Pacific Northwest National Laboratory=
Tel:=A0 509-372-6441 =



=A0

From: owner-ch= emistry+hubertus.vandam=3D=3D= pnnl.gov ~ ccl.net [ma= ilto:owner-chemistry+hubertus.vandam=3D=3Dpnnl.gov ~ cc= l.net] On Behalf Of Julien Thibault tchetchenko%gmail.com
Sent: Saturday, November 23, 2013 1:46 PM
To: Van Dam, Hub= ertus J
Subject: CCL: API for the Basis Set Exchange

=A0

Hi,=A0

I was wondering if anyb= ody was aware of an open-source distribution of the the basis set exchange = database (http= s://bse.pnl.gov/bse/portal) so that people can install it locally and/o= r access the database through an API (REST? Java?)

Regards,

~Julien

=A0

--=
Julien Thibault
University of Utah
Department of Biomedical Inf= ormatics
Salt Lake City, UT

=



--
Julien= Thibault
University of Utah
Department of Biomedical InformaticsSalt Lake City, UT
--e89a8ff24d9b1c131d04ec06fb5a-- From owner-chemistry@ccl.net Mon Nov 25 18:26:00 2013 From: "Diana O Rourke diana.orourke..certara.com" To: CCL Subject: CCL: SYBYL-X 2.1.1 has been released Message-Id: <-49378-131125182045-14830-MIm+GacTAQtbcqK5SQJpfQ::server.ccl.net> X-Original-From: "Diana O Rourke" Date: Mon, 25 Nov 2013 18:20:44 -0500 Sent to CCL by: "Diana O Rourke" [diana.orourke=-=certara.com] SYBYL-X 2.1.1 is now available for all customers with current support contracts. New functionality in this release includes augmented capabilities available via the standalone PYTHON interface to 3D-QSAR, which was introduced in SYBYL-X 2.1 earlier this year. The PYTHON API allows 3D-QSAR models (CoMFA, CoMSIA, and Topomer CoMFA) to be created and used for predictions outside of SYBYL-X, allowing you to create new QSAR workflows and incorporate 3D-QSAR into your corporate workflows, and easily integrate 3D QSAR predictions into your informatics desktops. New in SYBYL-X 2.1.1: 1. Hologram QSAR (HQSAR) is a now available via Python. HQSAR has been successfully applied to generate predictive global QSAR models for on- and off-target effects and models for important ADME related properties; the HQSAR method employs 2D-substructural counts as descriptors. 2. Similarity computations and similiarity searches (UNITY 2D fingerprints) are now accessible via Python to support various workflows, such as lead expansion, lead hopping, and cluster analysis. Additionally, this release addresses a number of customer reported issues. If youre a SYBYL-X customer and didnt get the announcement in your inbox last week, send a note to tripos.support[-]certara.com and we'll provide additional information. Best regards, Diana O'Rourke Marketing Director Certara diana.orourke[-]certara.com