From owner-chemistry@ccl.net Fri Jul 15 00:49:01 2011 From: "christina jenifer christinamsc]^[gmail.com" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45083-110715004125-26652-FHpsR4v0q2sqBfrv/lIpYw!A!server.ccl.net> X-Original-From: christina jenifer Content-Type: multipart/alternative; boundary=bcaec5215a4da75d4f04a814427f Date: Fri, 15 Jul 2011 10:11:17 +0530 MIME-Version: 1.0 Sent to CCL by: christina jenifer [christinamsc ~ gmail.com] --bcaec5215a4da75d4f04a814427f Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear zinebeladnani, * Thanks a lot for your answer. With Regards,* *CHRISTINA* On Fri, Jul 15, 2011 at 1:45 AM, zineb el adnani zinebeladnani/./hotmail.co= m wrote: > dear Christina > > > According to, the Koopmans=92 theorem for closed-shell molecules, ionizat= ion > energy I and electrons affinity A can be expressed in terms of the > highest occupied molecular orbital energy EHOMO, and the lowest unoccupie= d > molecular orbital energy ELUMO, respectively: > > A=3D- ELUMO > > I=3D-EHOMO > the absolute electronegativity X: > > X=3D1/( 2(I+A)) > > good luck > > > From: owner-chemistry|ccl.net > > To: zinebeladnani|hotmail.com > > Subject: CCL:G: How to calculate IP,EA,EN using Gaussian > > Date: Thu, 14 Jul 2011 13:50:51 -0400 > > > > > > > Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com] > > Dear all, > > > > I am wondering if anyone of you performed the following calculations fr= om > Gaussian output. How to calculate ionization potential, electron affinity > and electro negativity values from Gaussian output files and suggest me t= he > desired key word in order to calculate these values from output file. > > > > Any comments on this matter would be greatly appreciated > > > > Thanks in advance > > > > By > > > > CHRISTINA > > > > > > > > -=3D This is automatically added to each message by the mailing script = =3D- > > To recover the email address of the author of the message, please chang= e > > the strange characters on the top line to the | sign. You can also> > > > E-mail to subscribers: CHEMISTRY|ccl.net or use: > > > > > > E-mail to administrators: CHEMISTRY-REQUEST|ccl.net or use> > > > > --bcaec5215a4da75d4f04a814427f Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Dear zinebeladnani,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 Thanks a lot for your answer.

With Regards,

CHRIS= TINA

On Fri, Jul 15, 2011 at 1:45 AM,= zineb el adnani zinebeladnani/./hotmail.com= <owner= -chemistry!=!ccl.net> wrote:

dear Christina


According to, the Koopmans=92 theorem= for closed-shell molecules, ionization energy I and = =A0electrons affinity A can be expressed in terms of the highest occupied molecular orb= ital energy EHOMO, and the lowest unoccupied=A0 molecular orbital energy ELUMO, respectively:

<= p>A=3D- ELUMO

I=3D-EHOM= O

the absolute electronegativity = X:

X=3D1/( 2(I+A))

good luck

&g= t; From: owner-chemistry|ccl.n= et
> To: zinebeladnani|hot= mail.com
> Subject: CCL:G: How to calculate IP,EA,EN using Gaussi= an
> Date: Thu, 14 Jul 2011 13:50:51 -0400

> =
>
> Sent to CCL by: "christina jenifer g" [christinamsc= ]![gmail.com]
> De= ar all,
>
> I am wondering if anyone of you performed the fol= lowing calculations from Gaussian output. How to calculate ionization poten= tial, electron affinity and electro negativity values from Gaussian output = files and suggest me the desired key word in order to calculate these value= s from output file.
>
> Any comments on this matter would be greatly appreciated
= >
> Thanks in advance
>
> By
>
> CHRIST= INA
>
>
>
> -=3D This is automatically added to = each message by the mailing script =3D-
> To recover the email address of the author of the message, please chan= ge
> the strange characters on the top line to the | sign. You can al= so
>
> > E-mail to subscribers: CHEMISTRY|ccl.net or use:
>
>
>= ; E-mail to administrators: CHEMISTRY-REQUEST|ccl.net or use
>
>
>
> http://www.ccl.= net/chemistry/sub_unsub.shtml
>
> Before posting, check wa= it time at: http://www.ccl= .net
>
> Job: ht= tp://www.ccl.net/jobs
> Conferences: http://server= .ccl.net/chemistry/announcements/conferences/
>
> Search Messages: http://www.ccl.net/chemistry/searchccl= /index.shtml
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> If your mail bounces from CCL with 5.7.1 = error, check:
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>
> RTFI: http://www.= ccl.net/chemistry/aboutccl/instructions/
>
>

--bcaec5215a4da75d4f04a814427f-- From owner-chemistry@ccl.net Fri Jul 15 03:16:00 2011 From: "nicho demus mnichodemus*o*yahoo.com" To: CCL Subject: CCL:G: aim 2000 and wfn,wfx files -reg Message-Id: <-45084-110714125353-2308-LS5YaTn8HICpOQ/6h6zyNA],[server.ccl.net> X-Original-From: nicho demus Content-Type: multipart/alternative; boundary="0-315962647-1310662420=:84832" Date: Thu, 14 Jul 2011 22:23:40 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: nicho demus [mnichodemus#,#yahoo.com] --0-315962647-1310662420=:84832 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Thank you verymuch to Dr.Zaki safi and antoniochana for their kind.now i ca= n able to generae .wfn files, and it works well with AIMAll. with regards=20 Nichodemus m --- On Wed, 13/7/11, Antonio Chana achana*iqfr.csic.es wrote: > From: Antonio Chana achana*iqfr.csic.es Subject: CCL:G: aim 2000 and wfn,wfx files -reg To: "Maria Arockiam, Nichodemus " Date: Wednesday, 13 July, 2011, 4:30 AM Sent to CCL by: Antonio Chana [achana%iqfr.csic.es] Hi Nichodemus, Make sure you put the .wfn file name at the end of the gaussian input, leav= ing a blank line between the end of your input and the file name. Besides I= always use out=3Dwfn instead of output and it usually works in providing a= wfn file suitable for AIM2000. Regards, Antonio El 13/07/2011 7:17, Nichodemus Mariaarockiam mnichodemus()yahoo.com escribi= =F3: > Sent to CCL by: "Nichodemus=A0 Mariaarockiam" [mnichodemus+/-yahoo.com] > Hi researchers, i just want to use AIM 2000.while using the keyword outpu= t=3Dwfn in G03,link become broken and i dont get the proper wfn files. > then,i convert the .chk files into .fchk files=A0 and fed into aim which = also not works.even i open the converted wfn files, the dialouge shows "not= a compatible traditional aim file".what is the proper way of generating an= d using wfn files in AIM2000.Thanks in advance. > Nichodemus.M> >=20 >=20 -- Antonio Chana, Ph.D. Investigador contratado Departamento de Estructura, Energ=EDa y Reactividad Qu=EDmica INSTITUTO DE QUIMICA-FISICA "ROCASOLANO" Consejo Superior de Investigaciones Cient=EDficas Serrano 119 , E-28006 Madrid (Spain) Telf.: +34 91 5619400 Ext 1213 Fax.: +34 91 5642431 -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0=A0=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message Subscribe/Unsubscribe:=A0 =A0 =A0 http://www.ccl.net/chemistry/sub_unsub.sh= tmlConferences: http://server.ccl.net/chemistry/a= nnouncements/conferences/=A0 =A0=A0=A0http://www.ccl.net/spammers.txt--0-315962647-1310662420=:84832 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Thank you verymuch to Dr.Zaki safi and a= ntoniochana for their kind.now i can able to generae .wfn files, and it wor= ks well with AIMAll.
with regards
Nichodemus m

--- On Wed, 13/7/11, Antonio Chana achana*iqfr.= csic.es <owner-chemistry,+,ccl.net> wrote:

From: Antonio Chana achana*iqfr.csic.es <owner= -chemistry,+,ccl.net>
Subject: CCL:G: aim 2000 and wfn,wfx files -regTo: "Maria Arockiam, Nichodemus " <mnichodemus,+,yahoo.com>Date: Wednesday, 13 July, 2011, 4:30 AM


Sent to CCL by: Antonio Chana [achana%iqfr.csic.= es]
Hi Nichodemus,

Make sure you put the .wfn file name at the en= d of the gaussian input, leaving a blank line between the end of your input= and the file name. Besides I always use out=3Dwfn instead of output and it= usually works in providing a wfn file suitable for AIM2000.

Regards= ,

Antonio


El 13/07/2011 7:17, Nichodemus Mariaarockiam mn= ichodemus()yahoo.com escribi=F3:
> Sent to CCL by: "Nichodemus  = Mariaarockiam" [mnichodemus+/-yahoo.com]
> Hi researchers, i just wan= t to use AIM 2000.while using the keyword output=3Dwfn in G03,link become b= roken and i dont get the proper wfn files.
> then,i convert the .chk = files into .fchk files  and fed into aim which also not works.even i o= pen the converted wfn files, the dialouge shows "not a compatible tradition= al aim file".what is the proper way of generating and using wfn files in AIM2000.Thanks in advance.
> Nichodemus.M>
>
>
<= BR>
-- Antonio Chana, Ph.D.

Investigador contratado
Departamen= to de Estructura, Energ=EDa y Reactividad Qu=EDmica
INSTITUTO DE QUIMICA= -FISICA "ROCASOLANO"
Consejo Superior de Investigaciones Cient=EDficasSerrano 119 , E-28006 Madrid (Spain)
Telf.: +34 91 5619400 Ext 1213Fax.: +34 91 5642431



-=3D This is automatically added to ea= ch message by the mailing script =3D-
To recover the email address of th= e author of the message, please change
the strange characters on the top= line to the ,+, sign. You can also
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--0-315962647-1310662420=:84832-- From owner-chemistry@ccl.net Fri Jul 15 04:11:00 2011 From: "uekstrom .. gmail.com uekstrom .. gmail.com" To: CCL Subject: CCL: libquadmaths and Gfortran Message-Id: <-45085-110715040938-13161-9Mn8eBeOvKthsqLZDbviHw**server.ccl.net> X-Original-From: "uekstrom\a/gmail.com" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 15 Jul 2011 10:09:31 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom * gmail.com" [uekstrom * gmail.com] Perhaps this is not very helpful, but unless Gamess is explicitly designed to use higher precision arithmetics you cannot simply change the float types and expect it to work out of the box. The reason is that there are many algorithms that implicitly depend on the precision. One example would be the two electron integrals, which are typically computed to some accuracy that may be hard coded in the program. Another problem may be that the code may assume that each number requires eight bytes of memory. This is important for MPI communication and other external libraries. I am sorry if this is not relevant for Gamess, which perhaps explicitly supports arbitrary scalar types? In that case I think you should consult with the Gamess US people. Sincerely, Ulf Ekström From owner-chemistry@ccl.net Fri Jul 15 05:27:00 2011 From: "james robinson jameschums^^yahoo.com" To: CCL Subject: CCL: libquadmaths and Gfortran Message-Id: <-45086-110715052330-5939-NM+zviJIZc73rzhPZw5xfg\a/server.ccl.net> X-Original-From: james robinson Content-Type: multipart/alternative; boundary="0-1313292945-1310721801=:88886" Date: Fri, 15 Jul 2011 02:23:21 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: james robinson [jameschums{}yahoo.com] --0-1313292945-1310721801=:88886 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Thanks Ulf,=0A=0AI was wondering about using lidquadmaths with GamessUS, NW= chem and other fortran codes. Thank you for the helpful suggestions and I w= ill see what results I get from tinkering around. =0A=0A=0ARegards=0A=0AJam= es=0A=0A=0A=0A________________________________=0AFrom: uekstrom .. gmail.co= m uekstrom .. gmail.com =0ATo: "Robinson, James -i= d#3zx-" =0ASent: Friday, July 15, 2011 9:09 AM=0ASubj= ect: CCL: libquadmaths and Gfortran=0A=0A=0ASent to CCL by: "uekstrom * gma= il.com" [uekstrom * gmail.com]=0APerhaps this is not very helpful, but unle= ss Gamess is explicitly=0Adesigned to use higher precision arithmetics you = cannot simply change=0Athe float types and expect it to work out of the box= . The reason is=0Athat there are many algorithms that implicitly depend on = the=0Aprecision. One example would be the two electron integrals, which are= =0Atypically computed to some accuracy that may be hard coded in the=0Aprog= ram. Another problem may be that the code may assume that each=0Anumber req= uires eight bytes of memory. This is important for MPI=0Acommunication and = other external libraries. I am sorry if this is not=0Arelevant for Gamess, = which perhaps explicitly supports arbitrary=0Ascalar types? In that case I = think you should consult with the Gamess=0AUS people.=0A=0ASincerely,=0AUlf= Ekstr=F6m=0A=0A=0A=0A-=3D This is automatically added to each message by t= he mailing script =3D-=0ATo recover the email address of the author of the = message, please change=0Athe strange characters on the top line to the .. si= gn. You can also=0A=0A= =0A=0A=A0 =A0 =A0 http://ww= w.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMI= STRY-REQUEST..ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/ccl/se= nd_ccl_message=0A=0A=0A=A0 =A0 =A0 http://www.ccl.ne= t/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: http:/= /www.ccl.net=0A=0A=0AConferences: http://serve= r.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: http:/= /www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces from= CCL with 5.7.1 error, check:=0A=A0 =A0 =A0= =0A=0A--0-1313292945-1310721801=:88886 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Thanks Ulf,

I was wondering about using lidqu= admaths with GamessUS, NWchem and other fortran codes. Thank you for the he= lpful suggestions and I will see what results I get from tinkering around. =

Regards

James

From: uekstrom .. gmail.com uekstrom .. g= mail.com <owner-chemistry..ccl.net>
To: "Robinson, James " <jameschums..yahoo.com>
Sent= : Friday, July 15, 2011 9:09 AM
Subject: CCL: libquadmaths and Gfortran

<= br>Sent to CCL by: "uekstrom * gmail.com" [uekstrom * gmail.com]
Perhaps= this is not very helpful, but unless Gamess is explicitly
designed to u= se higher precision arithmetics you cannot simply change
the float types= and expect it to work out of the box. The reason is
that there are many= algorithms that implicitly depend on the
precision. One example would b= e the two electron integrals, which are
typically computed to some accur= acy that may be hard coded in the
program. Another problem may be that t= he code may assume that each
number requires eight bytes of memory. This= is important for MPI
communication and other external libraries. I am s= orry if this is not
relevant for Gamess, which perhaps explicitly supports arbitrary
scalar types? In that case I think you should consul= t with the Gamess
US people.

Sincerely,
Ulf Ekstr=F6m

<= br>
-=3D This is automatically added to each message by the mailing scri= pt =3D-
To recover the email address of the author of the message, pleas= e change
the strange characters on the top line to the .. sign. You can a= lso
E-mail = to subscribers: CHEMISTRY..ccl.net or use:
      htt= p://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administr= ators: CHEMISTRY-REQUEST..ccl.net or use
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<= br
      http://www.ccl.net/chemi= stry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job= : http://www.ccl.net/= jobs
Conferences: http://server.ccl.net/chemistry/ann= ouncements/conferences/

Search Messages: http://www.ccl.ne= t/chemistry/searchccl/index.shtml

If your mail bounces from CCL = with 5.7.1 error, check:
      http://www.ccl.net/spammers.txt
=
RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



--0-1313292945-1310721801=:88886-- From owner-chemistry@ccl.net Fri Jul 15 06:47:00 2011 From: "Y. Yuan echemistry(!)yahoo.com" To: CCL Subject: CCL: substructure search Message-Id: <-45087-110715064453-17096-OaJC3SQby+alT0+DmFFRqQ]![server.ccl.net> X-Original-From: "Y. Yuan" Content-Type: multipart/alternative; boundary="0-563468783-1310726683=:3097" Date: Fri, 15 Jul 2011 03:44:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Y. Yuan" [echemistry,+,yahoo.com] --0-563468783-1310726683=:3097 Content-Type: text/plain; charset=us-ascii CDK is the most famous open source one. Tony Yuanwww.scilligence.comOLN, Chem4SharePoint, JSDraw, MolEngine, MolSql --- On Thu, 7/14/11, Anurag Passi anuragpassibioinfo**gmail.com wrote: > From: Anurag Passi anuragpassibioinfo**gmail.com Subject: CCL: substructure search To: "Yuan, Tony " Date: Thursday, July 14, 2011, 3:11 PM Hello all, Can anyone tell me any open source softwares for doing similarity searching (substructure/fragment). Regards, -- Anurag Passi Project Assistant, OSDD, CSIR 00-91-9899767938 skype: anurag.passi --0-563468783-1310726683=:3097 Content-Type: text/html; charset=us-ascii
CDK is the most famous open source one.


Tony Yuan
www.scilligence.com
OLN, Chem4SharePoint, JSDraw, MolEngine, MolSql


--- On Thu, 7/14/11, Anurag Passi anuragpassibioinfo**gmail.com <owner-chemistry|ccl.net> wrote:

From: Anurag Passi anuragpassibioinfo**gmail.com <owner-chemistry|ccl.net>
Subject: CCL: substructure search
To: "Yuan, Tony " <echemistry|yahoo.com>
Date: Thursday, July 14, 2011, 3:11 PM

Hello all,

Can anyone tell me any open source softwares for doing similarity searching (substructure/fragment).

Regards,
--
Anurag Passi
Project Assistant, OSDD, CSIR
00-91-9899767938
skype: anurag.passi

--0-563468783-1310726683=:3097-- From owner-chemistry@ccl.net Fri Jul 15 07:59:00 2011 From: "Jussi Lehtola jussi.lehtola[A]helsinki.fi" To: CCL Subject: CCL: libquadmaths and Gfortran Message-Id: <-45088-110715063513-12982-wfj7sD7Fi0lDGmsq44M44g]|[server.ccl.net> X-Original-From: Jussi Lehtola Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 15 Jul 2011 13:35:00 +0300 Mime-Version: 1.0 Sent to CCL by: Jussi Lehtola [jussi.lehtola- -helsinki.fi] On Fri, 15 Jul 2011 02:23:21 -0700 (PDT) "james robinson jameschums^^yahoo.com" wrote: > Thanks Ulf, > > I was wondering about using lidquadmaths with GamessUS, NWchem and > other fortran codes. Thank you for the helpful suggestions and I will > see what results I get from tinkering around. libquadmaths is just a library. The keyword here is quad precision. Now, it totally depends on the code how easy it is to make it use a higher precision. For instance, sanely written Fortran 90 code defines data types as integer, parameter :: rk=selected_real_kind(10,40) ! Double precision or in a less portable format as integer, parameter :: rk=8 In the simplest case scenario, upgrading the precision would be as easy as increasing the value of rk. In the worst case scenario, everything is hard-coded, and the code needs to be ported to support a higher precision. Of course, as has been mentioned already in the thread, you might not gain anything from a higher precision, if the algorithm only works at some (lower) precision. -- -------------------------------------------------------- Mr. Jussi Lehtola, M. Sc. Doctoral Student jussi.lehtola * helsinki.fi Department of Physics http://www.helsinki.fi/~jzlehtol University of Helsinki Office phone: +358 9 191 50 632 Finland -------------------------------------------------------- Jussi Lehtola, FM Tohtorikoulutettava jussi.lehtola * helsinki.fi Fysiikan laitos http://www.helsinki.fi/~jzlehtol Helsingin Yliopisto Työpuhelin: (0)9 191 50 632 -------------------------------------------------------- From owner-chemistry@ccl.net Fri Jul 15 08:34:00 2011 From: "Andrew Dalke dalke-.-dalkescientific.com" To: CCL Subject: CCL: substructure search Message-Id: <-45089-110715074106-4095-RDaKMk+0R+36bm1qU+J1EQ[*]server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Fri, 15 Jul 2011 13:41:18 +0200 Mime-Version: 1.0 (Apple Message framework v1084) Sent to CCL by: Andrew Dalke [dalke]=[dalkescientific.com] On Jul 15, 2011, at 12:44 PM, Y. Yuan echemistry(!)yahoo.com wrote: > CDK is the most famous open source one. Really? I thought it was OpenBabel. Which also has substructure and similarity search. http://openbabel.org/wiki/Main_Page Behind either of those in terms of popularity is RDKit. It supports substructure and similarity search. If you use that system then you likely want to use its PostgreSQL integration. (To say nothing of its KNIME integration.) http://www.rdkit.org/ A newcomer to the game is Indigo, with its Bingo cartridges for Oracle and Microsoft SQL Server. It also has KNIME integration. http://ggasoftware.com/opensource/indigo Andrew dalke(0)dalkescientific.com From owner-chemistry@ccl.net Fri Jul 15 09:09:00 2011 From: "Kyle Lutz kyle.r.lutz- -gmail.com" To: CCL Subject: CCL: substructure search Message-Id: <-45090-110715090025-21195-JjU6Jq1y6KP6D0u2BCVKlg_-_server.ccl.net> X-Original-From: Kyle Lutz Content-Type: multipart/alternative; boundary=000e0cd47bec178da604a81b3baf Date: Fri, 15 Jul 2011 09:00:15 -0400 MIME-Version: 1.0 Sent to CCL by: Kyle Lutz [kyle.r.lutz ~~ gmail.com] --000e0cd47bec178da604a81b3baf Content-Type: text/plain; charset=ISO-8859-1 Hi Anurag, The chemkit (http://www.chemkit.org) library is able to perform substructure searches. See the Molecule::isSubstructureOf() method ( http://doc.chemkit.org/api/classchemkit_1_1_molecule.html#a732de6b4acd46d6cefd3f68f87e818d8 ). The chemkit library is written in C++ and available under the BSD license. Cheers, Kyle Lutz On Thu, Jul 14, 2011 at 3:11 PM, Anurag Passi anuragpassibioinfo**gmail.com wrote: > Hello all, > > Can anyone tell me any open source softwares for doing similarity searching > (substructure/fragment). > > Regards, > -- > Anurag Passi > Project Assistant, OSDD, CSIR > 00-91-9899767938 > skype: anurag.passi > > --000e0cd47bec178da604a81b3baf Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi Anurag,

The chemkit (http://ww= w.chemkit.org) library is able to perform substructure searches. See th= e Molecule::isSubstructureOf() method (http://doc.chemkit.org/api/classchemkit_1_1_molecule.html#a732d= e6b4acd46d6cefd3f68f87e818d8).

The chemkit library is written in C++ and available under the BSD licen= se.

Cheers,
Kyle Lutz

On Thu, J= ul 14, 2011 at 3:11 PM, Anurag Passi anuragpassibioinfo**gmail.com <owner-chemistry^ccl.net<= /a>> wrote:
Hello all,

Can anyone tell me any ope= n source softwares for doing similarity searching (substructure/fragment).<= br>
Regards,
--
Anurag Passi
Project Assi= stant, OSDD, CSIR
00-91-9899767938
skype: anurag.passi


--000e0cd47bec178da604a81b3baf-- From owner-chemistry@ccl.net Fri Jul 15 11:44:00 2011 From: "Goncalo Justino jgcj(_)fct.unl.pt" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45091-110715052725-10143-CrBb7T2Hj1q2gv+hhBcqgg * server.ccl.net> X-Original-From: "Goncalo Justino" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 15 Jul 2011 10:27:14 +0100 (WEST) MIME-Version: 1.0 Sent to CCL by: "Goncalo Justino" [jgcj:-:fct.unl.pt] Hi, sometimes hoopman's approximation gives some weird values. in those cases you may need to use the energy of the different species involved in each process. for example, ionization potential would be G(radical cation) - G (neutral precursor) if u consider deltaS to be negligible (is it?), you can use H(rad cat) - H(neutral). you may also be interested only in vertical processes, in which the geometry of the neutral is frozen and only the electrons are moving in/out of the molecule, in that case you only need 1 geometry optimization and some single point calculations. depends on what you're after. regards, g. On Fri, July 15, 2011 05:41, christina jenifer christinamsc]^[gmail.com wrote: > Dear zinebeladnani, > > * Thanks a lot for your answer. > > With Regards,* > > *CHRISTINA* > > On Fri, Jul 15, 2011 at 1:45 AM, zineb el adnani > zinebeladnani/./hotmail.com > wrote: > >> dear Christina >> >> >> According to, the Koopmans’ theorem for closed-shell molecules, >> ionization >> energy I and electrons affinity A can be expressed in terms of the >> highest occupied molecular orbital energy EHOMO, and the lowest >> unoccupied >> molecular orbital energy ELUMO, respectively: >> >> A=- ELUMO >> >> I=-EHOMO >> the absolute electronegativity X: >> >> X=1/( 2(I+A)) >> >> good luck >> >> > From: owner-chemistry|ccl.net >> > To: zinebeladnani|hotmail.com >> > Subject: CCL:G: How to calculate IP,EA,EN using Gaussian >> > Date: Thu, 14 Jul 2011 13:50:51 -0400 >> >> > >> > >> > Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com] >> > Dear all, >> > >> > I am wondering if anyone of you performed the following calculations >> from >> Gaussian output. How to calculate ionization potential, electron >> affinity >> and electro negativity values from Gaussian output files and suggest me >> the >> desired key word in order to calculate these values from output file. >> > >> > Any comments on this matter would be greatly appreciated >> > >> > Thanks in advance >> > >> > By >> > >> > CHRISTINA >> > >> > >> > >> > -= This is automatically added to each message by the mailing script >> =- >> > To recover the email address of the author of the message, please >> change >> > the strange characters on the top line to the | sign. You can also> > >> > E-mail to subscribers: CHEMISTRY|ccl.net or use: >> > >> > >> > E-mail to administrators: CHEMISTRY-REQUEST|ccl.net or use> > >> > >> > -- Gonçalo Justino, Ph.D. ---------------------------------------------------- [Computational & Radical BioChemistry] Requimte/CQFB - Department of Chemistry Faculty of Sciences and Technology New University of Lisbon 2829-516 Caparica Portugal Phone: (+351) 212 948 300 ext. 10971 Fax: (+351) 212 948 550 ---------------------------------------------------- All saints have a past, all sinners have a future. From owner-chemistry@ccl.net Fri Jul 15 12:18:01 2011 From: "Utpal Sarkar utpalchemiitkgp*gmail.com" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45092-110715030247-14029-XYVgB2RjeYZeuKEuwYdl4g|-|server.ccl.net> X-Original-From: Utpal Sarkar Content-Type: multipart/alternative; boundary=90e6ba2121371811b404a8163ca7 Date: Fri, 15 Jul 2011 12:32:37 +0530 MIME-Version: 1.0 Sent to CCL by: Utpal Sarkar [utpalchemiitkgp++gmail.com] --90e6ba2121371811b404a8163ca7 Content-Type: text/plain; charset=ISO-8859-1 hi christine, there are two ways to calculate it. in one method you can use homo lomu energy and in other method you can use energy of the neutral species and its cataion and anion. best utpal On Thu, Jul 14, 2011 at 11:20 PM, christina jenifer g christinamsc__gmail.com wrote: > > Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com] > Dear all, > > I am wondering if anyone of you performed the following calculations > from Gaussian output. How to calculate ionization potential, electron > affinity and electro negativity values from Gaussian output files and > suggest me the desired key word in order to calculate these values from > output file. > > Any comments on this matter would be greatly appreciated > > Thanks in advance > > By > > CHRISTINA> > > --90e6ba2121371811b404a8163ca7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
hi christine, there are two ways to calculate it. in one method you ca= n use homo lomu energy and in other method you can use energy of the neutra= l species and its cataion and anion.
best
utpal

On Thu, Jul 14, 2011 at 11:20 PM, christin= a jenifer g christinamsc__gmail.= com <ow= ner-chemistry|-|ccl.net> wrote:

Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com]
Dear all,

=A0 =A0 =A0 =A0I am wondering if anyone of you performed the following cal= culations from Gaussian output. How to calculate ionization potential, elec= tron affinity and electro negativity values from Gaussian output files and = suggest me the desired key word in order to calculate these values from out= put file.

=A0 =A0 =A0 =A0Any comments on this matter would be greatly appreciated
Thanks in advance

By

CHRISTINA



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--90e6ba2121371811b404a8163ca7-- From owner-chemistry@ccl.net Fri Jul 15 16:23:01 2011 From: "Kalju Kahn kalju_._chem.ucsb.edu" To: CCL Subject: CCL: libquadmaths and Gfortran Message-Id: <-45093-110715152359-27091-fp5RFkf56gJuNxkprdWLsQ .. server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 15 Jul 2011 12:23:25 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju]~[chem.ucsb.edu] Dear James, I am probably pointing out the obvious, but most modern hardware supports up to 80-bits for floats. Thus, libquadmath has to do the calculations in software, at the cost of decreased performance. I recall seeing someone quoting 2-200 times slower. Considering that many QM codes are tuned to align data well with CPU and memory registers, I would think that if you start with a well-tuned QM program, performing 128-bit precison in software will be much slower than performing 64 or 80 bit operations on hardware. I suppose one can try to mix and match within a code; e.g. define floats as float128 in parts that need the high precision and do not suffer from significant performance loss, then take the results from this part and convert to float64, giving a value with 16-digit precision, which are then used as inputs in parts that cannot be effectively converted to quad precision. Of course, you will not gain the full quad precision, but maybe just enough for your purpose. As was said earlier, you would also need to adjust various convergence criteria (either in the program code or in the input); there is not much point of using quad precision if the integrals smaller that 1E-9 are discarded (i.e. ICUT in Gamess). Best luck and please let us know what you find out, Kalju > > Sent to CCL by: "james robinson" [jameschums%x%yahoo.com] > Dear all, > > I have recently installed Fedora15 onto a Dell XPS system with an eight > core processor. I have installed numerical libraries, gfortran and an RPM > called libquadmaths.rpm . > > http://gcc.gnu.org/onlinedocs/libquadmath/index.html#Top > > Does anyone know how to modify the install script to ensure that extra > precision is used during compilation by enabling the libquadmath library > functionality with gamess compilation using Gfortran? Or do I have go > through the Gamess-US code and change typedefs and constants to the types > used by libquadmaths? > >> From what I have read on the GCC site, it is suggestive of 128bit >> floating point arithmetic, but my system is Fedora16 64bit - is that >> correct? Comments and tips would be welcome. > > It may of course be that I am mistaken and should be more careful but I > really want to check that I am not being a lunatic. > > Kind regards > > James> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106