From owner-chemistry@ccl.net Tue Jun 2 00:46:00 2009 From: "hirdesh kumar hirdeshs8::gmail.com" To: CCL Subject: CCL: Software to calculate IC50 value Message-Id: <-39416-090602004307-26616-TCbATQXp7LPsZYB7ZF7MUg]=[server.ccl.net> X-Original-From: hirdesh kumar Content-Type: multipart/alternative; boundary=0016364272b59d4a98046b552c6d Date: Tue, 2 Jun 2009 09:01:11 +0530 MIME-Version: 1.0 Sent to CCL by: hirdesh kumar [hirdeshs8,gmail.com] --0016364272b59d4a98046b552c6d Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Autodock gives the prediction of IC50 value from binding energy.... njoy --0016364272b59d4a98046b552c6d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Autodock gives the prediction of IC50 value from binding energy....
njoy
--0016364272b59d4a98046b552c6d-- From owner-chemistry@ccl.net Tue Jun 2 04:24:01 2009 From: "Jamie Platts Platts**cardiff.ac.uk" To: CCL Subject: CCL: MGMS Silver Jubilee Prize - Call for Nominations Message-Id: <-39417-090602041341-1729-WHMdOwdiAMMuaDJQp+4Mzg{}server.ccl.net> X-Original-From: Jamie Platts Content-Type: multipart/alternative; boundary="=_alternative 002D2EE6802575C9_=" Date: Tue, 2 Jun 2009 09:13:30 +0100 MIME-Version: 1.0 Sent to CCL by: Jamie Platts [Platts . cardiff.ac.uk] This is a multipart message in MIME format. --=_alternative 002D2EE6802575C9_= Content-Type: text/plain; charset="US-ASCII" Dear CCL Nominations are invited for the Molecular Graphics and Modelling Society Silver Jubilee Prize, with a deadline of 15th September 2009. Self-nominations are welcome, as are resubmissions from anyone who has unsuccessfully applied in recent years. Full details of eligibility, previous winners, and how to apply can be found on the MGMS website at http://www.mgms.org/diary.htm Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts%a%cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy --=_alternative 002D2EE6802575C9_= Content-Type: text/html; charset="US-ASCII"
Dear CCL

Nominations are invited for the Molecular Graphics and Modelling Society Silver Jubilee Prize, with a deadline of 15th September 2009. Self-nominations are welcome, as are resubmissions > from anyone who has unsuccessfully applied in recent years.

Full details of eligibility, previous winners, and how to apply can be found on the MGMS website at http://www.mgms.org/diary.htm

Jamie

----------------------------------------------------------
Jamie Platts
School of Chemistry       Phone: +44 (0) 2920 874950
Cardiff University             Email: platts%a%cf.ac.uk
Park Place                       FAX:   +44 (0) 2920 874030
Cardiff CF10 3AT             www.cf.ac.uk/chemy --=_alternative 002D2EE6802575C9_=-- From owner-chemistry@ccl.net Tue Jun 2 13:18:00 2009 From: "Austin B. Yongye ayongye[*]chem.uga.edu" To: CCL Subject: CCL: Harmonic constraints in gaussian Message-Id: <-39418-090602124714-25745-3e8g15G3o6S5s7lXwLSf9A.:.server.ccl.net> X-Original-From: "Austin B. Yongye" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 2 Jun 2009 11:51:51 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: "Austin B. Yongye" [ayongye]~[chem.uga.edu] Hi everyone, Does anyone have an example file on how to impose harmonic constraints on a subset of atoms during optimization? Seems the initialHarmonic, chkHarmonic and readHarmonic apply constraints to the entire structure. Any help will be greatly appreciated. Thanks, Austin- PS. Responses can be sent to ybausty-at-yahoo-dot-com From owner-chemistry@ccl.net Tue Jun 2 15:23:01 2009 From: "Kadir Diri kadir a visual1.chem.pitt.edu" To: CCL Subject: CCL: PES library available for download Message-Id: <-39419-090601214551-31362-UGWA7olcgIvsdBin7CwE4Q|-|server.ccl.net> X-Original-From: Kadir Diri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 01 Jun 2009 17:44:46 -0700 MIME-Version: 1.0 Sent to CCL by: Kadir Diri [kadir.:.visual1.chem.pitt.edu] Unfortunately, currently we don't have a version that is compatible with gcc/g++, although there is some possibility about doing this in the future if we would get enough interest. However, please note that Intel offers free software for "non-commercial" use, and heavily discounted rates for "academic" use... kadir TJ O Donnell tjo-#-acm.org wrote: > > Sent to CCL by: "TJ O'Donnell" [tjo#,#acm.org] > This looks very useful. I don't have the Intel compiler and > the library looks to be incompatible with gcc/g++. > Is there a g++ comatible ezPES library available? > > TJ O'Donnell > > kadir kadir|visual1.chem.pitt.edu wrote: >> >> Sent to CCL by: kadir [kadir- -visual1.chem.pitt.edu] >> Dear Colleagues, >> >> A library of full-dimensional semi-global potential energy surfaces >> (PES) generated from ab initio calculations is available for download: >> http://iopenshell.usc.edu/downloads/ezpes/ >> >> The library (ezPES) contains pre-compiled binaries and PES data >> files, and can be easily integrated into your own program, e.g., for >> dynamics or spectroscopy calculations. >> >> Currently, the following PESs are available: C2H3, C3H2 (singlet and >> triplet), H4CF, HCOH+, HCOH, C2H2, CH3OH, H2CO, H3O2-, H3O+, H5O2+. >> We will be adding others as they become available. >> >> Enjoy! >> kadir >> >> >> ---------- >> Kadir Diri, PhD >> Research Scientist >> Department of Chemistry and iOpenShell Center >> SSC #401 >> University of Southern California >> Los Angeles, CA 90089-0482 >> -------------------------- >> >> Relativistic correction to Murphy's law: >> Whether things can go wrong or not, depends on your frame of reference. From owner-chemistry@ccl.net Tue Jun 2 18:30:00 2009 From: "Raphael Ribeiro raphaelri[]hotmail.com" To: CCL Subject: CCL: DFT+U Message-Id: <-39420-090602182914-24524-rBOA9gHi1Cm6lbpm2wlSjQ!^!server.ccl.net> X-Original-From: "Raphael Ribeiro" Date: Tue, 2 Jun 2009 18:29:10 -0400 Sent to CCL by: "Raphael Ribeiro" [raphaelri-*-hotmail.com] Is VASP the only electronic structure code availabe that can do DFT+U ? Thanks Raphael From owner-chemistry@ccl.net Tue Jun 2 19:05:00 2009 From: "Shikha Varma-O Brien shikha[#]accelrys.com" To: CCL Subject: CCL: ACCELRYS SCIENCE FORUMS 2009 - FREE EVENT Message-Id: <-39421-090602185538-4675-zwkDwrlmTdzbO2VyndkGsA^server.ccl.net> X-Original-From: "Shikha Varma-O Brien" Date: Tue, 2 Jun 2009 18:55:34 -0400 Sent to CCL by: "Shikha Varma-O Brien" [shikha~~accelrys.com] Four US Locations: Boston (June 9) Princeton (June 11) San Francisco (June 16) San Diego (June 18) Dear all, The Accelrys Science Forums will be held at four US locations during the month of June. We invite you to join us along with prominent scientific researchers from industry and academia for these one-day regional events where you will have the opportunity to: Learn how innovative computational solutions for modeling and simulation, informatics, and data integration & reporting are being successfully applied throughout the Pharmaceutical and Biotechnology industries. See talks from Pfizer, Hoffman-LaRoche, University of Massachusetts, Cytokinetics, Genentech, University of Michigan, Johnson& Johnson, and more Attend hands-on computer labs/live demos with Accelrys scientists to get an up-close look at the latest software solutions available to help address your research challenges. Strengthen business relationships by networking with scientists from your area. Full program details including detailed agendas can be found at: www.accelrys.com/scienceforums While attendance for these events is free-of-charge, we encourage you to reserve your place early as spaces are limited. DATES/LOCATIONS June 9 Boston, MA Register and Get Further Details: http://cts.vresp.com/c/?Accelrys/a303c8cb3d/TEST/9c4a4e30aa June 11 Princeton, NJ Register and Get Further Details: http://cts.vresp.com/c/?Accelrys/a303c8cb3d/TEST/e982372913 June 16 San Francisco, CA Register and Get Further Details: http://cts.vresp.com/c/?Accelrys/a303c8cb3d/TEST/4f97342cf6 June 18 San Diego, CA Register and Get Further Details: http://cts.vresp.com/c/?Accelrys/a303c8cb3d/TEST/d1987b34bd We look forward to welcoming you to the 2009 Accelrys Science Forums. Please feel free to contact me with any questions. Best regards, Shikha _________________________________ Shikha Varma-O'Brien, Ph.D. Director, LS Modeling and Simulations Accelrys, Inc. http://www.accelrys.com __________________________________ From owner-chemistry@ccl.net Tue Jun 2 20:08:01 2009 From: "Jing Kong jkong/./q-chem.com" To: CCL Subject: CCL: Q-Chem Workshop in Washington D.C. Message-Id: <-39422-090602185647-5172-WP29zbg7pUH/vTYl1lkD1g a server.ccl.net> X-Original-From: "Jing Kong" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0338_01C9E3AE.AD785950" Date: Tue, 2 Jun 2009 18:19:08 -0400 MIME-Version: 1.0 Sent to CCL by: "Jing Kong" [jkong!^!q-chem.com] This is a multi-part message in MIME format. ------=_NextPart_000_0338_01C9E3AE.AD785950 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear colleague, Q-Chem Inc. would like to invite you to the workshop entitled "Quantum leap into the future: advances and applications of QM and QM/MM methods". The workshop will take place on 15th of August 2009 (Saturday), at NIH Bethesda campus in Washington DC area, the day before the Fall National ACS meeting. At the workshop, leaders in academia and government institutions will present new and improved computational methods for a wide range of chemical and biological applications. In addition, a hands-on tutorial session will provide ample opportunities to learn basic and advanced features of the state-of-the-art computational tools in Q-Chem, including QM/MM calculations with the popular MD program CHARMM. Invited speakers of our workshop (in alphabetical order): * Dr. Bernard Brooks (NIH) on new QM/MM methods with Q-Chem and CHARMM * Prof. Martin Head-Gordon (University of California, Berkeley) on new DFT and MP2 methods * Dr. Edina Rosta (NIH) on QM/MM applications * Dr. Jing Kong (Q-Chem Inc.) on new DFT algorithms and dispersion model * Dr. Qin Wu (Brookhaven National Lab) on charge-constrained DFT Interested parties please register at http://www.q-chem.com/wsd_regist.html till the 5th of August. Please bring your own laptop computers (Windows or MacOS) for the tutorials. Software for the tutorials will be provided through downloading prior to the workshop. Please note that this is the only announcement we will send out about this workshop. Please save this email and the link "http://www.q-chem.com/wsd_hh.html " for your future reference. I apologize if you have received multiple copies of this email. We look forward to seeing you at the workshop. Sincerely, Jing Kong, Ph.D. CEO & Chief Scientist ------=_NextPart_000_0338_01C9E3AE.AD785950 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear = colleague,

Q-Chem Inc. = would like to invite you to the workshop entitled "Quantum leap into the future: advances and applications of QM and QM/MM methods". The workshop = will take place on 15th of August 2009 (Saturday), at NIH Bethesda campus in = Washington DC area, the day before the Fall National ACS meeting. At the workshop, = leaders in academia and government institutions will present new and improved computational methods for a wide range of chemical and biological = applications. In addition, a hands-on tutorial session will provide ample = opportunities to learn basic and advanced features of the state-of-the-art computational = tools in Q-Chem, including QM/MM calculations with the popular MD program = CHARMM.

Invited = speakers of our workshop (in alphabetical order):

  • Dr. Bernard Brooks (NIH) on new QM/MM methods with Q-Chem and CHARMM =
  • Prof. Martin Head-Gordon (University = of California, Berkeley)  on new DFT and = MP2 methods
  • Dr. Edina Rosta (NIH) on QM/MM applications
  • Dr. Jing Kong (Q-Chem Inc.) on new DFT algorithms and dispersion model =
  • Dr. Qin Wu (Brookhaven National Lab) on charge-constrained DFT =

Interested = parties please register at http://www.q-chem.com/wsd_regist.html till the 5th of August.  Please bring your own laptop computers = (Windows or MacOS) for the tutorials. Software for the tutorials will be provided through downloading prior to the workshop.

Please note = that this is the only announcement we will send out about this workshop.  Please = save this email and the link “http://www.q-chem.com/wsd_hh.html<= /a>” for your future reference.

I apologize if = you have received multiple copies of this email.

We look = forward to seeing you at the workshop.

Sincerely, =

Jing Kong, Ph.D.
CEO & Chief Scientist

------=_NextPart_000_0338_01C9E3AE.AD785950-- From owner-chemistry@ccl.net Tue Jun 2 22:01:01 2009 From: "Yun Wang wangyun22[*]yahoo.com" To: CCL Subject: CCL: DFT+U Message-Id: <-39423-090602215301-19366-Fb6F9LPm7gfPrelA5BzhAA{:}server.ccl.net> X-Original-From: Yun Wang Content-Type: multipart/alternative; boundary="0-659226467-1243990368=:58171" Date: Tue, 2 Jun 2009 17:52:48 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Yun Wang [wangyun22],[yahoo.com] --0-659226467-1243990368=:58171 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable PWscf=0Awww.pwscf.org=0A=0A=0A=0A=0A________________________________=0AFrom= : Raphael Ribeiro raphaelri[]hotmail.com =0ATo: "W= ang, Yun " =0ASent: Wednesday, 3 June, 2009 8:= 29:10 AM=0ASubject: CCL: DFT+U=0A=0A=0ASent to CCL by: "Raphael Ribeiro" [= raphaelri-*-hotmail.com]=0AIs VASP the only electronic structure code avail= abe that can do DFT+U ?=0A=0AThanks=0ARaphael=0A=0A=0A=0A-=3D This is autom= atically added to each message by the mailing script =3D-=0ATo recover the = email address of the author of the message, please change=0Athe strange cha= racters on the top line to the : sign. You can also=0Alook up the X-Origina= l-From: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTRY : ccl.= net or use:=0A=0A=0AE-= mail to administrators: CHEMISTRY-REQUEST : ccl.net or use=0A http://www= .ccl.net/cgi-bin/ccl/send_ccl_message=0A=0A=0A ==0A=0ABefore posting, check wai= t time at: http://www.ccl.net=0A=0A=0AConferen= ces: http://server.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 http://www.ccl.net/s= pammers.txt=0A=0A= =0A=0A=0A Need a Holiday? Win a $10,000 Holiday of your choice. Enter = now.http://us.lrd.yahoo.com/_ylc=3DX3oDMTJxN2x2ZmNpBF9zAzIwMjM2MTY2MTMEdG1f= ZG1lY2gDVGV4dCBMaW5rBHRtX2xuawNVMTEwMzk3NwR0bV9uZXQDWWFob28hBHRtX3BvcwN0YWd= saW5lBHRtX3BwdHkDYXVueg--/SIG=3D14600t3ni/**http%3A//au.rd.yahoo.com/mail/t= agline/creativeholidays/*http%3A//au.docs.yahoo.com/homepageset/%3Fp1=3Doth= er%26p2=3Dau%26p3=3Dmailtagline --0-659226467-1243990368=:58171 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

From: Raphael Ribeiro raphaelri[]hotmail.com <owner-chemistry : ccl.net&g= t;
To: "Wang, Yun -id#3= tu-" <wangyun22 : yahoo.com>
S= ent: Wednesday, 3 June, 2009 8:29:10 AM
Subject: CCL: DFT+U


Sent to C= CL by: "Raphael  Ribeiro" [raphaelri-*-hotmail.com]
Is VASP the onl= y electronic structure code availabe that can do DFT+U ?

Thanks
Raphael


-=3D This is automatically added to each message by the mailing s= cript =3D-
To recover the email address of the author of the message, pl= ease change
the strange characters on the top line to the : sign. You ca= n also
E-ma= il to subscribers: CHEMISTRY : ccl.net or use:
      =

E-mail to admini= strators: CHEMISTRY-REQUEST : ccl.net or use
  &nb= sp;   http://www.ccl.net/cgi-bin/ccl/send_ccl_message
<= br
      http://www.ccl.net/chemi= stry/sub_unsub.shtml

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

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RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



=0A=0A=0A=0A
=0ANeed a Holiday? Win a = $10,000 Holiday of your choice. Enter now.. --0-659226467-1243990368=:58171-- From owner-chemistry@ccl.net Tue Jun 2 22:35:01 2009 From: "Ed Brothers ChicoraEd**gmail.com" To: CCL Subject: CCL: Amino Acid Polymorphism. Message-Id: <-39424-090602182524-24269-yYkV2SNAfK89jSw11g4Tog[-]server.ccl.net> X-Original-From: "Ed Brothers" Date: Tue, 2 Jun 2009 18:25:20 -0400 Sent to CCL by: "Ed Brothers" [ChicoraEd#%#gmail.com] Howdy! I have recently become interested in predicting the relative energies of various polymorphs of drugs and/or amino acids, in order to validate some new PBC work my coworkers and I have done. For example, there are three polymorphs of crystallized glycine, and we'd like to see if our tools can predict the relative stabilities (or at least get the correct order) of the three crystal structures. To do this validation, we are looking for a data set. Specifically, what we would love to find would be a set of crystal geometries (with translation vectors) for a given compound along with experimental relative energies or at least energy ordering. I started poking around in the literature to find such as set, and rapidly found the volume of literature on this topic daunting. Because of this I'd like to appeal to the expertise of the CCL. Is there a standard test case for this, or can someone recommend a valid test set? Thanks for your time, Ed Brothers Visiting Assistant Professor Texas A&M at Qatar PS I will summarize for the list.