From owner-chemistry@ccl.net Thu Jul 14 07:31:01 2011 From: "Rajarshi Guha rajarshi.guha-#-gmail.com" To: CCL Subject: CCL: Call for Submissions: CINFLash (ACS National Meeting, Denver, Fall 2011) Message-Id: <-45076-110714073009-10842-3xs+nifVXEjhEeHodtPgsA===server.ccl.net> X-Original-From: Rajarshi Guha Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 14 Jul 2011 07:30:02 -0400 MIME-Version: 1.0 Sent to CCL by: Rajarshi Guha [rajarshi.guha_._gmail.com] The ACS Division of Chemical Information (CINF) will be holding an experimental symposium on Wednesday, August 31, at the ACS National Meeting in Denver, titled CINFlash. The symposium will be composed of lightning talks - each talk will be 8 minutes each and will be *strictly* timed. There is no specific topic, but we expect talks to focus on cheminformatics and chemical information. Most importantly, we are not using the ACS abstract submission system (PACS) and instead will be directly collecting short abstracts uptil August 14. As a result, we hope talks will present recent developments and we expect that talks will not rehash material from a year ago or be verbal versions of posters already submitted for the meeting. Abstracts should be submitted to cinf.flash-*-gmail.com. To maintain the flow of the symposium we will require slide decks before the meeting so we can set up the machine for smooth transitions. Visit http://acscinf.org/meetings/242/calls/flash242.php for more details. If you have any questions mail me at rajarshi.guha-*-gmail.com -- Rajarshi Guha NIH Chemical Genomics Center From owner-chemistry@ccl.net Thu Jul 14 08:10:01 2011 From: "Guha, Rajarshi (NIH/NHGRI) C guhar%mail.nih.gov" To: CCL Subject: CCL: Call for Submissions: CINFLash (ACS National Meeting, Denver, Fall 2011) Message-Id: <-45077-110714072309-16315-jD7o1Y8CvgcWISP6NXIMiw:-:server.ccl.net> X-Original-From: "Guha, Rajarshi (NIH/NHGRI) [C]" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 14 Jul 2011 07:22:57 -0400 MIME-Version: 1.0 Sent to CCL by: "Guha, Rajarshi (NIH/NHGRI) [C]" [guhar^^mail.nih.gov] The ACS Division of Chemical Information (CINF) will be holding an experimental symposium on Wednesday, August 31, at the ACS National Meeting in Denver, titled CINFlash. The symposium will be composed of lightning talks - each talk will be 8 minutes each and will be *strictly* timed. There is no specific topic, but we expect talks to focus on cheminformatics and chemical information. Most importantly, we are not using the ACS abstract submission system (PACS) and instead will be directly collecting short abstracts uptil August 14. As a result, we hope talks will present recent developments and we expect that talks will not rehash material from a year ago or be verbal versions of posters already submitted for the meeting. Abstracts should be submitted to cinf.flash|*|gmail.com. To maintain the flow of the symposium we will require slide decks before the meeting so we can set up the machine for smooth transitions. Visit http://acscinf.org/meetings/242/calls/flash242.php for more details. If you have any questions mail me at rajarshi.guha|*|gmail.com ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- From owner-chemistry@ccl.net Thu Jul 14 10:02:01 2011 From: "Alina Osnis alina_roz*hotmail.com" To: CCL Subject: CCL: Potential Energy Distribution (PED) analysis of normal modes Message-Id: <-45078-110714095847-14004-af2QHl5My/Co8vNXzGQpcA*server.ccl.net> X-Original-From: "Alina Osnis" Date: Thu, 14 Jul 2011 09:58:44 -0400 Sent to CCL by: "Alina Osnis" [alina_roz.:.hotmail.com] Hello, I would like to do a Potential Energy Distribution (PED) analysis of normal modes. Could someone help me with a detailed mathematical description of how to do this: (i.e. the structure of the matrices I need to use. I want to do this with Matlab)? I know that some programs can do this, but I need to implement it by myself for use with a specific software we have. Thank you very much, Alina Osnis (PhD) Chemistry Department Bar-Ilan University e-mail:alina_roz===hotmail.com From owner-chemistry@ccl.net Thu Jul 14 10:40:01 2011 From: "james robinson jameschums .. yahoo.com" To: CCL Subject: CCL: libquadmaths and Gfortran Message-Id: <-45079-110714103926-27446-HntZAFwxcmuGWKnvpTZAvQ{}server.ccl.net> X-Original-From: "james robinson" Date: Thu, 14 Jul 2011 10:39:23 -0400 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 From owner-chemistry@ccl.net Thu Jul 14 13:54:00 2011 From: "christina jenifer g christinamsc__gmail.com" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45080-110714135111-13526-hWftBNX52aXUfe5SnR2MIQ]![server.ccl.net> X-Original-From: "christina jenifer g" 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 From owner-chemistry@ccl.net Thu Jul 14 17:45:01 2011 From: "Anurag Passi anuragpassibioinfo**gmail.com" To: CCL Subject: CCL: substructure search Message-Id: <-45081-110714151109-1725-nzeXCRrDdzyEbVeo7mHnaw:+:server.ccl.net> X-Original-From: Anurag Passi Content-Type: multipart/alternative; boundary=0015175885123a7b2904a80c4bd0 Date: Fri, 15 Jul 2011 00:41:02 +0530 MIME-Version: 1.0 Sent to CCL by: Anurag Passi [anuragpassibioinfo_-_gmail.com] --0015175885123a7b2904a80c4bd0 Content-Type: text/plain; charset=ISO-8859-1 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 --0015175885123a7b2904a80c4bd0 Content-Type: text/html; charset=ISO-8859-1 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

--0015175885123a7b2904a80c4bd0-- From owner-chemistry@ccl.net Thu Jul 14 18:19:00 2011 From: "zineb el adnani zinebeladnani/./hotmail.com" To: CCL Subject: CCL:G: How to calculate IP,EA,EN using Gaussian Message-Id: <-45082-110714161542-7258-23scL8dPMiSwJC/URtcTQw .. server.ccl.net> X-Original-From: zineb el adnani Content-Type: multipart/alternative; boundary="_3d2b1d0f-4828-4191-9a55-2f2203fd7147_" Date: Thu, 14 Jul 2011 20:15:32 +0000 MIME-Version: 1.0 Sent to CCL by: zineb el adnani [zinebeladnani||hotmail.com] --_3d2b1d0f-4828-4191-9a55-2f2203fd7147_ Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable dear Christina According to=2C the Koopmans=92 theorem for closed-shell molecules=2C ionization energy I and electrons affinity A can be expressed in terms of the highest= occupied molecular orbital energy EHOMO=2C and the lowest unoccupied=20 molecular orbital energy ELUMO=2C respectively:A=3D- ELUMOI=3D-EHOMO the absolute electronegativity X: X=3D1/( 2(I+A)) good luck > From: owner-chemistry!A!ccl.net > To: zinebeladnani!A!hotmail.com > Subject: CCL:G: How to calculate IP=2CEA=2CEN using Gaussian > Date: Thu=2C 14 Jul 2011 13:50:51 -0400 >=20 >=20 > Sent to CCL by: "christina jenifer g" [christinamsc]![gmail.com] > Dear all=2C >=20 > I am wondering if anyone of you performed the following calculations fro= m Gaussian output. How to calculate ionization potential=2C electron affini= ty and electro negativity values from Gaussian output files and suggest me = the desired key word in order to calculate these values from output file. >=20 > Any comments on this matter would be greatly appreciated >=20 > Thanks in advance >=20 > By >=20 > CHRISTINA >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message=2C please chang= e>=20>=20>=20 > Subscribe/Unsubscribe:=20>=20 > Before posting=2C check wait time at: http://www.ccl.net >=20 > Job: http://www.ccl.net/jobs=20>=20>=20 > If your mail bounces from CCL with 5.7.1 error=2C check:>=20>=20 >=20 = --_3d2b1d0f-4828-4191-9a55-2f2203fd7147_ Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

dear Christina


<= /span>

Accordi= ng to=2C the Koopmans=92 theorem for closed-shell molecul= es=2C ionization energy I and &n= bsp=3Belectrons affinity A can be expressed in terms of the highest occupied molecular orbital energy EHOMO=2C and the lowest unoccupied =3B molecular orbital energy ELUMO=2C respectively:

A=3D- ELUMO

I=3D-EHOMO

the absolute electronegativity X:<= br>
X=3D1/( 2(I+A))

good luck

>=3B From:= owner-chemistry!A!ccl.net
>=3B To: zinebeladnani!A!hotmail.com
>=3B = Subject: CCL:G: How to calculate IP=2CEA=2CEN using Gaussian
>=3B Date= : Thu=2C 14 Jul 2011 13:50:51 -0400
>=3B
>=3B
>=3B Sent to= CCL by: "christina jenifer g" [christinamsc]![gmail.com]
>=3B Dear al= l=2C
>=3B
>=3B I am wondering if anyone of you performed the fo= llowing calculations from Gaussian output. How to calculate ionization pote= ntial=2C electron affinity and electro negativity values from Gaussian outp= ut files and suggest me the desired key word in order to calculate these va= lues from output file.
>=3B
>=3B Any comments on this matter wo= uld be greatly appreciated
>=3B
>=3B Thanks in advance
>=3B=
>=3B By
>=3B
>=3B CHRISTINA
>=3B
>=3B
>= =3B
>=3B -=3D This is automatically added to each message by the mail= ing script =3D-
>=3B To recover the email address of the author of the= message=2C please change
>=3B the strange characters on the top line = to the !A! sign. You can also
>=3B look up the X-Original-From: line in = the mail header.
>=3B
>=3B E-mail to subscribers: CHEMISTRY!A!ccl.= net or use:
>=3B=
>=3B
>=3B E-mail to administrators: CHEMISTRY-REQUEST!A!ccl.net o= r use
>=3B
&g= t=3B
>=3B
>=3B http://www.ccl.net/= chemistry/sub_unsub.shtml
>=3B
>=3B Before posting=2C check wait= time at: http://www.ccl.net
>=3B
>=3B Job: http://www.ccl.net/j= obs
>=3B Conferences: http://server.ccl.net/chemistry/announcements/c= onferences/
>=3B
>=3B Search Messages: http://www.ccl.net/chemis= try/searchccl/index.shtml
>=3B
>=3B If your mail bounces from CC= L with 5.7.1 error=2C check:
>=3B http://www.ccl.net/spammers.tx= t
>=3B
>=3B RTFI: http://www.ccl.net/chemistry/aboutccl/instruct= ions/
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>=3B
= --_3d2b1d0f-4828-4191-9a55-2f2203fd7147_--