From owner-chemistry@ccl.net Mon Oct 8 03:09:01 2007 From: "omar Deeb deeb2000il]_[yahoo.com" To: CCL Subject: CCL: Drug design course Message-Id: <-35339-071007071321-2021-vtWbBYciVCbXBg/QELHZqA[#]server.ccl.net> X-Original-From: omar Deeb Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1976519956-1191751990=:19460" Date: Sun, 7 Oct 2007 03:13:10 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: omar Deeb [deeb2000il-x-yahoo.com] --0-1976519956-1191751990=:19460 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCL users, I would like to give a drug design course to the 5th year Pharmacy students. I will appreciate any comments or suggestions concerning this course including textbook, lecture notes, handouts, power point presentation, excercises ...etc Thanks in advance Dr. Omar Deeb Al-Quds University Jerusalem --------------------------------- Tonight's top picks. What will you watch tonight? Preview the hottest shows on Yahoo! TV. --0-1976519956-1191751990=:19460 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear CCL users,
I would like to give a drug design course to the 5th year Pharmacy students.
I will appreciate any comments or suggestions concerning this course including textbook, lecture notes, handouts, power point presentation, excercises ...etc
 
Thanks in advance
 
Dr. Omar Deeb
Al-Quds University
Jerusalem


Tonight's top picks. What will you watch tonight? Preview the hottest shows on Yahoo! TV. --0-1976519956-1191751990=:19460-- From owner-chemistry@ccl.net Mon Oct 8 03:44:01 2007 From: "Dhurairajan Senthilnathan zenthil03#,#yahoo.co.in" To: CCL Subject: CCL:G: Key for orbital overlap printing option Message-Id: <-35340-071008032622-8650-srHnOKG6H0Ny4oemO79SvQ ~~ server.ccl.net> X-Original-From: "Dhurairajan Senthilnathan" Date: Mon, 8 Oct 2007 03:26:18 -0400 Sent to CCL by: "Dhurairajan Senthilnathan" [zenthil03-$-yahoo.co.in] Dear CCLrs, I want to print the value of variation of orbital overlap(Sij) as a function of internuclear distance (rij) in my output file (using Gaussian 98). please tell me the best basis set or IOP option for overlap matrix display in my optput file. thank in advance D.Senthilnathan From owner-chemistry@ccl.net Mon Oct 8 06:07:01 2007 From: "may abdelghani may01dz|*|yahoo.fr" To: CCL Subject: CCL: a small imaginarily frequency Message-Id: <-35341-071008060357-28525-D339fVZUgIHm149P7W9dbA.:.server.ccl.net> X-Original-From: "may abdelghani" Date: Mon, 8 Oct 2007 06:03:53 -0400 Sent to CCL by: "may abdelghani" [may01dz-x-yahoo.fr] dear CCLers A unique imaginarily frequency of -57 cm-1 is enough to say, that the corresponding structure is a transition states and not another local minima? The task was be a transition states search. From owner-chemistry@ccl.net Mon Oct 8 08:26:00 2007 From: "Nuno A. G. Bandeira nuno.bandeira[a]ist.utl.pt" To: CCL Subject: CCL: a small imaginarily frequency Message-Id: <-35342-071008082336-10632-SjXKadwOWugm3TVqtdhirQ++server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 08 Oct 2007 13:23:10 +0100 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira|a|ist.utl.pt] may abdelghani may01dz|*|yahoo.fr wrote: > Sent to CCL by: "may abdelghani" [may01dz-x-yahoo.fr] > dear CCLers > A unique imaginarily frequency of -57 cm-1 is enough to say, that the > corresponding structure is a transition states and not another local > minima? The task was be a transition states search. If it's not a weak interaction you're dealing with then I'd say it's a minimum. Just so you know there have been "minima" reported in the literature with as much as -300 cm-1. But the usual arbitrary guideline is discard imaginary frequencies between 0 and -100 cm-1. They generally can be put off as computational error within DFT. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student [] IST,Lisbon -- From owner-chemistry@ccl.net Mon Oct 8 09:06:00 2007 From: "Andreas Bick andreas.bick..scienomics.com" To: CCL Subject: CCL: Help for MD simulation of metal cluster on substrate Message-Id: <-35343-071008064421-25094-wsnrIz4h9JBtcKiA0WIDVg ~~ server.ccl.net> X-Original-From: Andreas Bick Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 08 Oct 2007 12:02:52 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Bick [andreas.bick[*]scienomics.com] Dear Uptal, try LAMMPS (http://lammps.sandia.gov/) , this should be able to provide the needed functionality. Best regards Andreas > Dear CCL Users, > I want to use free molecular dynamics code to do the > simulation of metal cluster (say Iron > or Na) on substrate (say silicon). I want to know which molecular > dynamics code can do it (specially to > optimize the structures)? I also want to know is there any option in > the code where I can implement > my own potential energy function (or force field)? > > I will be highly obliged if you can give me some advise. > > Thanking you in advance > With best regards > Utpal Sarkar -- Dr. Andreas Bick Scienomics SARL Sales and Marketing mobile: +491621309945 From owner-chemistry@ccl.net Mon Oct 8 10:12:00 2007 From: "Michel Petitjean ptitjean/a\itodys.jussieu.fr" To: CCL Subject: CCL: linux64 free pgms Message-Id: <-35344-071008094347-23146-irNF9CJ5flXG6+syao41SQ-.-server.ccl.net> X-Original-From: Michel Petitjean Date: Mon, 8 Oct 2007 14:55:00 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean~~itodys.jussieu.fr] To: chemistry~~ccl.net Subj: linux64 free pgms Hi CCLers, The following free programmes are now available for linux 64 bits: ARMS : RMS alignment (known pairwise correspondence) + 3D common motif ASV : van der Waals surfaces and volumes (analytic and/or Monte-Carlo) CSR : 3D alignment (computes pairwise correspondence) + 3D common motif DOG : geometric docking (known pairwise correspondence) POP : optimal partition (classification) ; exists also in "R" QCM : degree of chirality of a conformer (computes graph automorphisms) RADI : computes convex hull, radius, diameter, and various shape coefficients RADI2 : same as RADI, and computes minimal size (enclosing planes) These programmes are also available for linux 32 bits, DEC-alphastations, macosx, SGI (6 architectures), IBM-RS6000, and SUN (SPARC and X64). Hope it helps. Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096) CEA Saclay, bat. 528 91191 Gif-sur-Yvette Cedex Phone: +33(0)1 6908 9681 / Fax: +33(0)1 6908 4007 E-mail: petitjean~~itodys.jussieu.fr http://petitjeanmichel.free.fr/itoweb.petitjean.html Formerly: ITODYS (CNRS, UMR 7086), 1 rue Guy de la Brosse, 75005 Paris, France. From owner-chemistry@ccl.net Mon Oct 8 11:33:01 2007 From: "Chris Howard c.k.howard a reading.ac.uk" To: CCL Subject: CCL: Help for MD simulation of metal cluster on substrate Message-Id: <-35345-071008112102-18722-2NbaQmdzjXHCm+8GjNpz2w__server.ccl.net> X-Original-From: Chris Howard Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 08 Oct 2007 15:33:09 +0100 Mime-Version: 1.0 Sent to CCL by: Chris Howard [c.k.howard]=[reading.ac.uk] Hi Uptal. A powerful alternative is the DL_POLY 2 code: http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ it is free to Academia. All the best, Chris On Oct 8 2007, Andreas Bick andreas.bick..scienomics.com wrote: > >Sent to CCL by: Andreas Bick [andreas.bick[*]scienomics.com] >Dear Uptal, > >try LAMMPS (http://lammps.sandia.gov/) , this should be able to provide >the needed functionality. > >Best regards > >Andreas > >> Dear CCL Users, >> I want to use free molecular dynamics code to do the >> simulation of metal cluster (say Iron >> or Na) on substrate (say silicon). I want to know which molecular >> dynamics code can do it (specially to >> optimize the structures)? I also want to know is there any option in >> the code where I can implement >> my own potential energy function (or force field)? >> >> I will be highly obliged if you can give me some advise. >> >> Thanking you in advance >> With best regards >> Utpal Sarkar > > > > From owner-chemistry@ccl.net Mon Oct 8 14:33:00 2007 From: "Qian Wang xie.wang^gmail.com" To: CCL Subject: CCL: can I specify charge in VASP? Message-Id: <-35346-071008142401-23984-mIEgMjoUoCy79UMqIYzFdw,+,server.ccl.net> X-Original-From: "Qian Wang" Content-Type: multipart/alternative; boundary="----=_Part_349_11743819.1191864539097" Date: Mon, 8 Oct 2007 13:28:59 -0400 MIME-Version: 1.0 Sent to CCL by: "Qian Wang" [xie.wang^^gmail.com] ------=_Part_349_11743819.1191864539097 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline > Dear all, > > Just curious, how do I calculate a charged periodic system in VASP? Is > there a place to specify charge and multiplicity? > > Thanks a lot! > > Xie Wang > ------=_Part_349_11743819.1191864539097 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear all,

Just curious, how do I calculate a charged periodic system in VASP? Is there a place to specify charge and multiplicity?

Thanks a lot!

Xie Wang

------=_Part_349_11743819.1191864539097-- From owner-chemistry@ccl.net Mon Oct 8 15:07:00 2007 From: "venkat n nvenkat83~~yahoo.co.in" To: CCL Subject: CCL: Drug design course Message-Id: <-35347-071008062753-5957-ubKBCpHyTvdU1vpIxYHHBA*|*server.ccl.net> X-Original-From: venkat n Content-Type: multipart/alternative; boundary="0-98414426-1191835934=:67506" Date: Mon, 8 Oct 2007 15:02:14 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: venkat n [nvenkat83()yahoo.co.in] --0-98414426-1191835934=:67506 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable dear sir,=0Ait is very progrmme. make the course to be online so that we al= so will learn from your presentations.=0A =0A*****************************= =0A N. Venkatramaiah=0Ac/o Dr.R. Venkatesan Research Scholar=0A Dept. o= f Chemistry=0A Pondicherry University=0A Pondicherry-605014=0A *********= *********************=0A=0A=0A----- Original Message ----=0AFrom: omar Deeb= deeb2000il]_[yahoo.com =0ATo: "Nutalapati, Venkma= tramaiah " =0ASent: Sunday, 7 October, 2007 = 3:43:10 PM=0ASubject: CCL: Drug design course=0A=0ADear CCL users,=0A I wo= uld like to give a drug design course to the 5th year Pharmacy students.=0A= I will appreciate any comments or suggestions concerning this course incl= uding textbook, lecture notes, handouts, power point presentation, excercis= es ...etc=0A =0A Thanks in advance=0A =0A Dr. Omar Deeb=0A Al-Quds U= niversity=0A Jerusalem=0A =0A =0ATonight's top picks. What will you w= atch tonight? =0APreview the hottest shows on Yahoo! TV. =0A =0A=0A=0A=0A= =0A=0A Now you can chat without downloading messenger. Go to http://in= ..messenger.yahoo.com/webmessengerpromo.php --0-98414426-1191835934=:67506 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
dear sir,
it is very progrmme. make the course to be onl= ine so that we also will learn from your presentations.
 
*****************************
N.= Venkatramaiah
c/o Dr.R. Venkatesan
Research Scholar
De= pt. of Chemistry
Pondicherry University
Pondicherry-605014
=
******************************


----- Original Message ----
From: omar Deeb deeb2000il]_[yahoo.com &= lt;owner-chemistry,+,ccl.net>
To: "Nutalapati, Venkmatramaiah "= <nvenkat83,+,yahoo.co.in>
Sent: Sunday, 7 October, 2007 3:43:10 PM<= br>Subject: CCL: Drug design course

Dear CCL users,
I would like to give a drug design course to the 5th year Pharmacy student= s.
I will appreciate any comments or suggestions concerning thi= s course including textbook, lecture notes, handouts, power point presentat= ion, excercises ...etc
 
Thanks in advance
 
Dr. Omar Deeb
Al-Quds University
Jerusalem

=0A


Tonight's top pick= s. What will you watch tonight? =0APreview the hottest shows on Yahoo! TV. =0A

=0A=0A=0A
5, 50, 500= , 5000 - Store N number of mails in your inbox. Click here. --0-98414426-1191835934=:67506-- From owner-chemistry@ccl.net Mon Oct 8 16:27:01 2007 From: "Adam Hunter spacyhunter_._gmail.com" To: CCL Subject: CCL:G: Any atomic CI code with a high precision? Message-Id: <-35348-071008153708-9707-ZimWDxG6+muC48MoJ2hOcA\a/server.ccl.net> X-Original-From: Adam Hunter Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 08 Oct 2007 11:38:55 -0700 MIME-Version: 1.0 Sent to CCL by: Adam Hunter [spacyhunter+*+gmail.com] hi, all, Is there any atom CI code which can do very accurate calculations? I mean it can carry out CI (multi-reference prefered) calculations with Slater basis set, or it can do Hylleraas type variational calculations on atoms. Any program based on Gaussian basis set is not appropriate. Anybody knows about this? Thank you very much in advance! best regards Adam From owner-chemistry@ccl.net Mon Oct 8 21:19:01 2007 From: "Sina T reli sinatureli|gmail.com" To: CCL Subject: CCL: A Question About Z-Matrix and Mopac Inputs Message-Id: <-35349-071008211825-24971-jDQMNZPhiE960rJj+/LH7w!=!server.ccl.net> X-Original-From: "Sina T reli" Date: Mon, 8 Oct 2007 21:18:22 -0400 Sent to CCL by: "Sina T reli" [sinatureli-x-gmail.com] Hello, I want to run a calculation with mopac in which I need to freeze some atoms. I was looking at the FAQ of mopac and it says in the z-matrix input format there are two types of information, one of which is the atomic coordinates which should supposedly be in the form: H -1.31 1 0.12 1 1.89 1 where if I change the 1's to 0's the atoms will be frozen. However the only information in the Z-matrix files are in the form of H 1.092 1 120.615 1 179.979 1 10 9 11 which state the bond distances, angles and dihedgral angles of the given atom to other atoms. I tried to create both z-matrix and xyz files using hyperchem and downloaded some samples from the website but none of them seems to contain the atoms coordinate in the form given (xyz does contain coordinates but then it is only a list of coordinates with nothing, no 0's or 1's near the coordinates). How can I create mopac input files in which I can freeze atoms by the form given above? Thanks alot... From owner-chemistry@ccl.net Mon Oct 8 22:30:01 2007 From: "Steve Gwaltney drg51]|[ra.msstate.edu" To: CCL Subject: CCL:G: Any atomic CI code with a high precision? Message-Id: <-35350-071008190252-5288-Kgag8lIxvL3+EqNaX/G/SA|a|server.ccl.net> X-Original-From: Steve Gwaltney Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 08 Oct 2007 17:02:50 -0500 MIME-version: 1.0 Sent to CCL by: Steve Gwaltney [drg51/a\ra.msstate.edu] Many years ago I used the ATOMCI program of Sasaki and co-workers, which is designed to do multi-reference CI calculations on atoms using Slater functions. At the time the ATOMCI was available through IBM's MOTECC program, but a quick search did not yield any information about how to get it now. Steve Gwaltney Adam Hunter spacyhunter_._gmail.com wrote: > > Sent to CCL by: Adam Hunter [spacyhunter+*+gmail.com] > hi, all, > Is there any atom CI code which can do very accurate calculations? I > mean it can carry out CI (multi-reference prefered) calculations with > Slater basis set, or it can do Hylleraas type variational calculations > on atoms. Any program based on Gaussian basis set is not appropriate. > Anybody knows about this? Thank you very much in advance! > best regards > Adam -- Dr. Steven Gwaltney Phone: 662-325-7602 Assistant Professor Fax: 662-325-1618 Department of Chemistry, Mail: Box 9573 Center for Environmental Health Sciences, Mississippi State University and HPCC Center for Computational Sciences Mississippi State, MS 39762 From owner-chemistry@ccl.net Mon Oct 8 23:31:00 2007 From: "jinyao wang wangjy###ciac.jl.cn" To: CCL Subject: CCL:G: for help Message-Id: <-35351-071008074652-5471-4X4PxMtV4LHfK0NH/45eaA.:.server.ccl.net> X-Original-From: "jinyao wang" Date: Mon, 8 Oct 2007 07:46:49 -0400 Sent to CCL by: "jinyao wang" [wangjy|-|ciac.jl.cn] Hello, I am calculating the carbonyl vibration frequency of the acetone which is in the supercritical carbon dioxide. I have known the the carbonyl has interaction with carbon dioxide. In experiment,the carbonyl frequencies are various with the pressures of the supercritical carbon dioxide. I am wondering how to calculate these with GAUSSIAN03. Any advice is appreciated