From owner-chemistry@ccl.net Tue Sep 26 03:42:00 2006 From: "Bala Subramanian bala**igib.res.in" To: CCL Subject: CCL: polarisable force field for new molecule Message-Id: <-32621-060926033935-18380-yyiaQa/TLlivRPq0zoEFUw..server.ccl.net> X-Original-From: "Bala Subramanian" Date: Tue, 26 Sep 2006 03:39:34 -0400 Sent to CCL by: "Bala Subramanian" [bala|*|igib.res.in] Dear CCL users, I am working on nucleic acid-drug interaction. I am very new to this. I want to use polarisable force field to simulate the complex. I can use ff02 for my DNA in amber, but i dnt know how to generate polarisable ff for ligand or in general any new molecule.Someone please suggest me on how i can do this. Thanks, C.Bala From owner-chemistry@ccl.net Tue Sep 26 04:47:00 2006 From: "Igor Avilov avilovi,averell.umh.ac.be" To: CCL Subject: CCL:G: HOMO-LUMO energy gap for cation radical Message-Id: <-32622-060926044254-8806-6b+P/mbCMAU+jTA7HBNePg-#-server.ccl.net> X-Original-From: "Igor Avilov" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 26 Sep 2006 09:59:42 +0200 MIME-Version: 1.0 Sent to CCL by: "Igor Avilov" [avilovi[a]averell.umh.ac.be] Dear Agalya, It is indeed a question how to define the HOMO/LUMO gap for cation radical. In the case when the molecule has a set of doubly occupied and "fully" unoccupied orbitals, it is, of cause, clear how to do that. And then the value of this HOMO/LUMO energy gap may be compared to, for example, the lowest energy transition of the molecule. In the radical cation an electron may be promoted, for example, from the singly-occupied orbital to some unfilled orbital, or from some doubly occupied orbital (in the restricted open shell treatment) to singly occupied orbital. Thus, if you are interested in the excited states' properties it is better to perform, on my opinion, TD-DFT calculation for your radical cation. So the question is: what experimental data you want to explain? Best regards, Igor. -----Original Message----- > From: owner-chemistry*|*ccl.net [mailto:owner-chemistry*|*ccl.net] Sent: dimanche 24 septembre 2006 14:59 To: Igor Avilov Subject: CCL:G: HOMO-LUMO energy gap for cation radical Sent to CCL by: "Agalya G" [agalya81#%#gmail.com] Dear CCL users, In my previous message i made typing mistakes. Kindly answer for this question. I have a querry regarding HOMO-LUMO gap for cation radical system. I have performed calculations for neutral, cation radical and dication systems. 1) For neutral system, I used ( Charge=0 and spin multiplicity=1) 2) For cation radical system, I used ( Charge=+1 and spin multiplicity=2) 3) For dication, I used (charge=+2 and spin multiplicity=1) For neutal and dication systems, in gaussian03 program, it gives Occupied and Virtual orbital energies with alpha spin. For cation radical system, it gives occupied and unoccupied orbital energies for both alpha and beta spins. My querry is, how to compare HOMO-LUMO energy gaps between these systems. How to get HOMO-LUMO gap for cation radical system, in case i want to compare this value with HOMO-LUMO energy gap with neutral and dication systems. Kindly give me some suggestions. With Regards, Agalyahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Sep 26 07:46:00 2006 From: "Antoine FORTUNE Antoine.Fortune:-:ujf-grenoble.fr" To: CCL Subject: CCL: Queue Systems for Linux PC Cluster Message-Id: <-32623-060925090115-6613-yWapsPZpYetCX9Jp0yoyjg!A!server.ccl.net> X-Original-From: Antoine FORTUNE Content-Type: multipart/mixed; boundary="------------020007090606010907070606" Date: Mon, 25 Sep 2006 12:53:01 +0200 MIME-Version: 1.0 Sent to CCL by: Antoine FORTUNE [Antoine.Fortune]_[ujf-grenoble.fr] This is a multi-part message in MIME format. --------------020007090606010907070606 Content-Type: multipart/alternative; boundary="------------080902080409010702060205" --------------080902080409010702060205 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit We use OAR on our Linux cluster (14 bi-Xeon), and it goes very well for distributed or parallel computations ... Submission by command line or scripts and on-line/web/GUI to follow CPUs occupancy/vacancy My opinion : simple and efficient ... all I need. here is the OAR' URL : http://oar.imag.fr/ Bye, Antoine. Brian Salter-Duke b_duke*bigpond.net.au wrote: > Sent to CCL by: Brian Salter-Duke [b_duke.(0).bigpond.net.au] > > On Sat, Sep 23, 2006 at 01:12:40PM -0400, Sidney Ramos Santana santanasidney _ yahoo.com.br wrote: > >> Sent to CCL by: "Sidney Ramos Santana" [santanasidney=yahoo.com.br] >> Dear CCL Users, >> >> I would like to install a "Queue System" for an automatic >> >> control of "jobs" submission by programs as DLPOLY, >> >> NWCHEM, DALTON, COLUMBUS on a Linux PC Cluster. >> >> I would appreciate to know your opinions about >> >> this subject. >> >> So, what is the best Queue Systems for a Linux PC Cluster? >> > > I use my own - the Simple Queueing System:- > > http://sqs.sourceforge.net/ > > but then "I would, would'nt I". Seriously it is not that good, but I > would welcome comment. I plan to release a new version in October that > simplifies use on a cluster, but I am in UK at present and it will have > to wait until I get home on Oct 7th. > > It also depends on the number of users and number of jobs. Some systems > are over kill. > > Cheers, Brian. > > >> Thanks for any help! >> >> Best Regard, >> >> Sidney Ramos de Santana >> Theoretical and Computational Chemistry Lab. (LQTC) >> Fundamental Chemistry Depart. (DQF) >> Federal University of Pernambuco (UFPE) >> Recife - PE - Brazil >> e-mail: santanasidney_at_yahoo.com.br> >> >> >> > > --------------080902080409010702060205 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit We use OAR on our Linux cluster (14 bi-Xeon), and it goes very well for distributed or parallel computations ...
Submission by command line or scripts and on-line/web/GUI to follow CPUs occupancy/vacancy
My opinion : simple and efficient ... all I need.

here is the OAR' URL : http://oar.imag.fr/

Bye, Antoine.


Brian Salter-Duke b_duke*bigpond.net.au wrote: 
Sent to CCL by: Brian Salter-Duke [b_duke.(0).bigpond.net.au]

On Sat, Sep 23, 2006 at 01:12:40PM -0400, Sidney Ramos Santana santanasidney _ yahoo.com.br wrote:
  
Sent to CCL by: "Sidney Ramos Santana" [santanasidney=yahoo.com.br]
Dear CCL Users,

I would like to install a "Queue System" for an automatic

control of "jobs" submission by programs as DLPOLY,

NWCHEM, DALTON, COLUMBUS on a Linux PC Cluster.

I would appreciate to know your opinions about

this subject. 

So, what is the best Queue Systems for a Linux PC Cluster?
    

I use my own - the Simple Queueing System:-

http://sqs.sourceforge.net/

but then "I would, would'nt I". Seriously it is not that good, but I
would welcome comment. I plan to release a new version in October that
simplifies use on a cluster, but I am in UK at present and it will have
to wait until I get home on Oct 7th.

It also depends on the number of users and number of jobs. Some systems
are over kill.

Cheers, Brian.
 
  
Thanks for any help!

Best Regard,

Sidney Ramos de Santana
Theoretical and Computational Chemistry Lab. (LQTC)
Fundamental Chemistry Depart. (DQF)
Federal University of Pernambuco (UFPE)
Recife - PE - Brazil
e-mail: santanasidney_at_yahoo.com.br>
--------------080902080409010702060205-- --------------020007090606010907070606 Content-Type: text/x-vcard; charset=utf-8; name="Antoine.Fortune.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Antoine.Fortune.vcf" begin:vcard fn;quoted-printable:Antoine Fortun=C3=A9 n;quoted-printable: Fortun=C3=A9;Antoine org;quoted-printable:U. Joseph Fourier (Grenoble 1);Dept. Pharmacochimie Mol=C3=A9culaire - UMR 5063 UJF/CNRS adr:;;5 avenue de Verdun ;MEYLAN;;38240;FRANCE email;internet:Antoine.Fortune(0)ujf-grenoble.fr title;quoted-printable:Ing=C3=A9nieur d'Etude Mod=C3=A9lisation Mol=C3=A9culaire tel;work:+33 4 76 04 10 38 x-mozilla-html:TRUE url:http://dpm.ujf-grenoble.fr version:2.1 end:vcard --------------020007090606010907070606-- From owner-chemistry@ccl.net Tue Sep 26 09:14:00 2006 From: "Karol Langner karol.langner/./kn.pl" To: CCL Subject: CCL: Queue Systems for Linux PC Cluster Message-Id: <-32624-060926044756-10519-vj/eRwjKxq4DW6CL7oabVw**server.ccl.net> X-Original-From: Karol Langner Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 26 Sep 2006 09:47:44 +0200 MIME-Version: 1.0 Sent to CCL by: Karol Langner [karol.langner!=!kn.pl] Hi list, On Tuesday 26 of September 2006 04:09, Fenglou Mao fenglou+/-csbl.bmb.uga.edu wrote: > Sent to CCL by: "Fenglou Mao" [fenglou() csbl.bmb.uga.edu] > > We are using Sun Grid Engine, it is easy to install and easy to use, > compared with PBS, it is easier. One more important reason, in our system > PBS can only submit ~95% the jobs if you submit thousands of jobs by using > script, but Sun Grid Engine can do all. What do you mean by this? Do you mean that PBS cannot submit certain types of jobs, or that it can't handle such large queues? Cheers, Karol -- written by Karol Langner Tue Sep 26 09:46:37 CEST 2006 From owner-chemistry@ccl.net Tue Sep 26 09:49:01 2006 From: "Orlin Blajiev blajiev- -vub.ac.be" To: CCL Subject: CCL:G: Link in Gaussian Message-Id: <-32625-060926092155-19585-wwp8ngrHlYsoWuc4MhYpEw.:.server.ccl.net> X-Original-From: Orlin Blajiev Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 26 Sep 2006 14:28:15 +0200 MIME-Version: 1.0 Sent to CCL by: Orlin Blajiev [blajiev^_^vub.ac.be] Hi, I will very much appreciate if somebody lets me know what is wrong with the input for a multistep work so that I got the given error message. It is not memory as both steps work separately. The input: %chk=/u/blajiev/gauss/amtd/amtd.chk #T B3LYP/6-31G* opt=(maxcyc=200) gfprint pop=(full) XX amtd.pdb 0 1 N 3.157313 2.400971 0.000000 C 1.840648 2.280898 0.000000 N 1.570839 0.875138 0.000000 N -0.345408 -0.822575 0.000000 C -1.732359 -0.842589 0.000000 S -2.197813 -2.520605 0.000000 S 0.000000 0.744727 0.000000 H 3.793522 1.597308 0.000000 H 3.575380 3.321957 0.000000 H -3.532824 -2.309817 0.000000 --Link1-- %chk=/u/blajiev/gauss/amtd/amtd.chk %mem=200MW #T B3LYP/6-31G* freq Geom=Check iop(7/33=1) Freq The error: Redundant internal coordinates taken from checkpoint file: /u/blajiev/gauss/amtd/amtd.chk End of file in GetChg. Error termination via Lnk1e in /usr/local/products/g03/exe/l101.exe at Tue Sep 26 14:01:26 2006. Job cpu time: 0 days 0 hours 0 minutes 1.9 seconds. File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 7 Scr= 1 -- Orlin Blajiev Department of Metallurgy, Electrochemistry and Materials Science Faculty of Applied Science Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussels Belgium http://www.vub.ac.be/META/ tel.: 32-(0)2-6293538 fax : 32-(0)2-6293200 From owner-chemistry@ccl.net Tue Sep 26 11:44:00 2006 From: "Fenglou Mao fenglou:-:csbl.bmb.uga.edu" To: CCL Subject: CCL: Queue Systems for Linux PC Cluster Message-Id: <-32626-060926095429-28805-FghTnz87uRThZEpb/aHNEA _ server.ccl.net> X-Original-From: "Fenglou Mao" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 26 Sep 2006 08:54:25 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: "Fenglou Mao" [fenglou!A!csbl.bmb.uga.edu] If you have thousands of small jobs and you want to submit it by using a perl script, you will get into problems - some of them can not be submitted successfully. > Sent to CCL by: Karol Langner [karol.langner!=!kn.pl] > Hi list, > > On Tuesday 26 of September 2006 04:09, Fenglou Mao > fenglou+/-csbl.bmb.uga.edu > wrote: >> Sent to CCL by: "Fenglou Mao" [fenglou() csbl.bmb.uga.edu] >> >> We are using Sun Grid Engine, it is easy to install and easy to use, >> compared with PBS, it is easier. One more important reason, in our >> system >> PBS can only submit ~95% the jobs if you submit thousands of jobs by >> using >> script, but Sun Grid Engine can do all. > What do you mean by this? Do you mean that PBS cannot submit certain types > of > jobs, or that it can't handle such large queues? > > Cheers, > Karol > > -- > written by Karol Langner > Tue Sep 26 09:46:37 CEST 2006> > > > From owner-chemistry@ccl.net Tue Sep 26 12:41:00 2006 From: "Igor Filippov Contr igorf*_*helix.nih.gov" To: CCL Subject: CCL: Queue Systems for Linux PC Cluster Message-Id: <-32627-060926122520-1177-WDkPbahUhko+qyysdXN49g++server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 26 Sep 2006 10:45:51 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf-.-helix.nih.gov] On Tue, 2006-09-26 at 09:34, Karol Langner karol.langner/./kn.pl wrote: > Sent to CCL by: Karol Langner [karol.langner!=!kn.pl] > Hi list, > > On Tuesday 26 of September 2006 04:09, Fenglou Mao fenglou+/-csbl.bmb.uga.edu > wrote: > > Sent to CCL by: "Fenglou Mao" [fenglou() csbl.bmb.uga.edu] > > > > We are using Sun Grid Engine, it is easy to install and easy to use, > > compared with PBS, it is easier. One more important reason, in our system > > PBS can only submit ~95% the jobs if you submit thousands of jobs by using > > script, but Sun Grid Engine can do all. > What do you mean by this? Do you mean that PBS cannot submit certain types of > jobs, or that it can't handle such large queues? I believe PBS cannot handle large queues when a big number of jobs is submitted _at_once_. I have used OpenPBS and overall I cannot say that I would recommend it to anyone - I was surprised to hear that many other people found it otherwise. Perhaps they've been using the commercial fork - PBSpro, or some non-standard version of OpenPBS, but stock OpenPBS leaves a lot to be desired - problems with big job submissions are among the minor issues compared to the rest. I've never used PBSpro, but considering the open source version I'm not eager to try. My topmost problem with OpenPBS is the way it handles failed nodes - if a node is free, and for some reason - hardware problem etc. - it went down, PBS marks it as being down and doesn't distribute jobs to that node, everything as it should be. If, on the other hand, a node running a job failed - the whole queuing system will get stuck, you won't be able to submit a job, or check the status with qstat or even kill a job. The only way out is either to restart the PBS or fix the failed node - not the best way to have fault tolerance. Add to that jobs getting stuck in exit status ("E"), jobs getting stuck forever in queued status ("Q") and you might see that there are reasons to consider alternatives to PBS. Regards, Igor > > Cheers, > Karol From owner-chemistry@ccl.net Tue Sep 26 13:15:01 2006 From: "Alfred Gil agil[*]cesca.es" To: CCL Subject: CCL:G: Link in Gaussian Message-Id: <-32628-060926112035-10427-pzT5OgVGz/sw5S9TD+XpSQ**server.ccl.net> X-Original-From: Alfred Gil Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 26 Sep 2006 16:41:05 +0200 MIME-Version: 1.0 Sent to CCL by: Alfred Gil [agil!A!cesca.es] I think you forgot the charge and multiplicity line in the second input. Regards, En/na Orlin Blajiev blajiev- -vub.ac.be ha escrit: > Sent to CCL by: Orlin Blajiev [blajiev^_^vub.ac.be] > Hi, > > I will very much appreciate if somebody lets me know what is wrong with > the input for a multistep work so that I got the given error message. It > is not memory as both steps work separately. > > > The input: > %chk=/u/blajiev/gauss/amtd/amtd.chk > #T B3LYP/6-31G* opt=(maxcyc=200) gfprint pop=(full) > > XX amtd.pdb > > 0 1 > N 3.157313 2.400971 0.000000 > C 1.840648 2.280898 0.000000 > N 1.570839 0.875138 0.000000 > N -0.345408 -0.822575 0.000000 > C -1.732359 -0.842589 0.000000 > S -2.197813 -2.520605 0.000000 > S 0.000000 0.744727 0.000000 > H 3.793522 1.597308 0.000000 > H 3.575380 3.321957 0.000000 > H -3.532824 -2.309817 0.000000 > > --Link1-- > %chk=/u/blajiev/gauss/amtd/amtd.chk > %mem=200MW > #T B3LYP/6-31G* freq Geom=Check iop(7/33=1) > > Freq > > The error: > > Redundant internal coordinates taken from checkpoint file: > /u/blajiev/gauss/amtd/amtd.chk > End of file in GetChg. > Error termination via Lnk1e in /usr/local/products/g03/exe/l101.exe at > Tue Sep 26 14:01:26 2006. > Job cpu time: 0 days 0 hours 0 minutes 1.9 seconds. > File lengths (MBytes): RWF= 8 Int= 0 D2E= 0 Chk= 7 > Scr= 1 > > > -- ...................................................................... __ / / Alfred Gil i Arranz C E / S / C A Departament de Sistemes /_/ Centre de Supercomputació de Catalunya Gran Capitą, 2-4 (Edifici Nexus) · 08034 Barcelona T. 93 205 6464 · F. 93 205 6979 · agil*_*cesca.es ...................................................................... From owner-chemistry@ccl.net Tue Sep 26 13:50:00 2006 From: "Osman Guner oguner-*-turquoisecons.com" To: CCL Subject: CCL: AIMECS 07 Message-Id: <-32629-060926130717-19768-wToFffOt4I6qjERhGllbAg*|*server.ccl.net> X-Original-From: "Osman Guner" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C6E153.8AC661F0" Date: Tue, 26 Sep 2006 10:07:14 -0700 MIME-Version: 1.0 Sent to CCL by: "Osman Guner" [oguner-*-turquoisecons.com] This is a multi-part message in MIME format. ------=_NextPart_000_0007_01C6E153.8AC661F0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Are you starting to plan your conference schedule for 2007? Here is one conference you may want to put in your calendar for sure. =20 6th AFMC International Medicinal Chemistry Symposium 2007 ISTANBUL =20 Posted on behalf of the conference organizers: Ismail Yalcin, and Esin = Aki (Sener)=85 =20 =20 The previous conference organized by Ismail and Esin was EuroQSAR 04, = which broke all records (number of papers, posters, attendees, speakers, = etc.). So you can expect and excellent organization for AIMECS 07 as well. The = web site for the conference is http://www.aimecs07.org/=20 =20 Dear Colleagues, =20 It is a great honour for us to cordially invite you to AIMECS 07, the = 6th International Medicinal Chemistry Symposium organized by the Asian Federation of Medicinal Chemistry (AFMC), to be held in Istanbul, Turkey > from July 08-11, 2007. The previous five symposia were held in Tokyo = (1995), Seoul (1997), Beijing (1999), Brisbane (2001) and Kyoto (2003).=20 =20 The 6th AFMC International Medicinal Chemistry Symposium is going to = gather the medicinal chemists from all over the world by the contribution of = the European Federation of Medicinal Chemistry (EFMC) and the American = Chemical Society, Division of Medicinal Chemistry (ACSMC) as the participating organizations within this World Summit in Istanbul, the city that = bridges the two great continents Asia and Europe.=20 =20 The scope of =93Medicinal Chemistry=94 has undergone noteworthy and scientifically intriguing expansion in recent years. In the 21st = century, =93Drug Discovery and Development=94 are extremely important and = challenging themes and their solutions will bring tremendous practical benefits to humanity. Therefore AIMECS 07 will focus on the design, discovery and development of new pharmaceuticals and novel bioactive molecules. This symposium will include individual sessions on Chemistry, Pharmacology, = Drug Metabolism and Toxicology, and Physiology for Pharmaceuticals as well as Cheminformatics, Bioinformatics and other important topics on Drug = Discovery and Development.=20 =20 Besides the scientific aspects of the programme you will have a chance = to explore one of the most ancient metropolises of the world, Istanbul, = which, throughout the centuries, sheltered the oldest and greatest cultures and civilizations of the humanity and where three major empires ruled the = world > from this powerful capital, the Romans, the Byzantines and the Ottomans, = and each of these left their mark on Istanbul, both culturally and architecturally.=20 =20 All colleagues interested in receiving updated information about AIMECS = 07 Meeting are invited to register at Symposium web site www.aimecs07.org . = =20 We look forward to welcoming you to Istanbul in July, 2007, for AIMECS = 07. =20 Ismail YALCIN (Symposium Chairman) =20 Esin Aki (Sener) (Organizing Committee Chair) =20 =20 --- Osman F, G=FCner, PhD Principal, Turquoise Consulting oguner++turquoisecons.com=20 http://www.turquoisecons.com=20 Skype: turquoisecons =20 =20 ------=_NextPart_000_0007_01C6E153.8AC661F0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Are you starting to plan your conference schedule for = 2007?=A0 Here is one conference you may want to put in your calendar for = sure.

 

6th AFMC International Medicinal = Chemistry Symposium 2007 ISTANBUL<= /b>

 

Posted on behalf of the conference organizers: Ismail Yalcin, and Esin Aki (Sener)…=A0

 

The previous conference organized by Ismail and Esin = was EuroQSAR 04, which broke all records (number of papers, posters, = attendees, speakers, etc.).=A0 So you can expect and excellent organization for = AIMECS 07 as well.=A0 The web site for the conference is http://www.aimecs07.org/

 

Dear Colleagues,

 

It is a great honour for us to cordially invite you = to AIMECS 07, the 6th International Medicinal Chemistry Symposium organized = by the Asian Federation of Medicinal Chemistry (AFMC), to be held in Istanbul, Turkey > from July 08-11, 2007. The previous five symposia were held in Tokyo (1995), Seoul (1997), Beijing (1999), Brisbane (2001) and Kyoto (2003). =

 

The 6th AFMC International Medicinal Chemistry = Symposium is going to gather the medicinal chemists from all over the world by the = contribution of the European Federation of Medicinal Chemistry (EFMC) and the = American Chemical Society, Division of Medicinal Chemistry (ACSMC) as the = participating organizations within this World Summit in Istanbul, the city that = bridges the two great continents Asia and Europe.

 

The scope of “Medicinal Chemistry” has = undergone noteworthy and scientifically intriguing expansion in recent years. In = the 21st century, “Drug Discovery and Development” are extremely = important and challenging themes and their solutions will bring tremendous = practical benefits to humanity. Therefore AIMECS 07 will focus on the design, = discovery and development of new pharmaceuticals and novel bioactive molecules. = This symposium will include individual sessions on Chemistry, Pharmacology, = Drug Metabolism and Toxicology, and Physiology for Pharmaceuticals as well as Cheminformatics, Bioinformatics and other important topics on Drug = Discovery and Development.

 

Besides the scientific aspects of the programme you = will have a chance to explore one of the most ancient metropolises of the = world, Istanbul, which, throughout the centuries, sheltered the oldest and = greatest cultures and civilizations of the humanity and where three major empires = ruled the world from this powerful capital, the Romans, the Byzantines and the Ottomans, and each of these left their mark on Istanbul, both culturally = and architecturally.

 

All colleagues interested in receiving updated = information about AIMECS 07 Meeting are invited to register at Symposium web site = www.aimecs07.org .

 

We look forward to welcoming you to Istanbul in July, 2007, for AIMECS = 07.

 

Ismail YALCIN

(Symposium Chairman)=A0=A0=A0=A0 =

Esin Aki (Sener)

(Organizing Committee = Chair)

 

 

---

Osman F, G=FCner, PhD

Principal, Turquoise = Consulting

oguner++turquoisecons.com&nbs= p;

http://www.turquoisecons.com&nb= sp;

Skype: turquoisecons

 

 

------=_NextPart_000_0007_01C6E153.8AC661F0-- From owner-chemistry@ccl.net Tue Sep 26 14:25:01 2006 From: "Daria Khvostichenko dkhvosti]^[uiuc.edu" To: CCL Subject: CCL:G: Link in Gaussian Message-Id: <-32630-060926141401-30484-q4FDFhQhG0FXpa+wXfOsug : server.ccl.net> X-Original-From: "Daria Khvostichenko" Date: Tue, 26 Sep 2006 14:14:01 -0400 Sent to CCL by: "Daria Khvostichenko" [dkhvosti{=}uiuc.edu] Orlin, I think you just don't have enough blank lines in the end of the input file. Try at to have at least two. Gaussian defaults to zero charge and singlet multiplicity (when possible) if those are not specified in the input file. Daria From owner-chemistry@ccl.net Tue Sep 26 15:00:01 2006 From: "Adlane Sayede adlane.sayede,,gmail.com" To: CCL Subject: CCL:G: Gaussian 03 and XEON 64-bit Message-Id: <-32631-060926064712-3890-Syki4vbhKk85DmoW2h2ghQ(!)server.ccl.net> X-Original-From: "Adlane Sayede" Date: Tue, 26 Sep 2006 06:47:11 -0400 Sent to CCL by: "Adlane Sayede" [adlane.sayede^^gmail.com] I am trying to compile Gaussian 03 Rev. B05, on Linux with Intel XEON 64-bit, without success. I have both PGI and IFC compilers. Can someone please give me some advice? Thank you in advance. P.S. : My search in the archive list has been not fruitful !!!!!!!!!! Adlane From owner-chemistry@ccl.net Tue Sep 26 15:35:01 2006 From: "Adlane sayede adlane.sayede]_[gmail.com" To: CCL Subject: CCL:G: Gaussian 03 and XEON 64-bit Message-Id: <-32632-060926074754-9831-Zv9rANGh3iGFFqKRrWpOxQ*server.ccl.net> X-Original-From: "Adlane sayede" Content-Type: multipart/alternative; boundary="----=_Part_3642_30796383.1159267781878" Date: Tue, 26 Sep 2006 12:49:41 +0200 MIME-Version: 1.0 Sent to CCL by: "Adlane sayede" [adlane.sayede^_^gmail.com] ------=_Part_3642_30796383.1159267781878 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline I am trying to compile Gaussian 03 Rev. B05, on Linux with Intel XEON 64-bit, without success. I have both PGI and IFC compilers. Can someone please give me some advice? Thank you in advance. P.S. : My search in the archive list has been not fruitful !!!!!!!!!! Adlane ------=_Part_3642_30796383.1159267781878 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline 
I am trying to compile Gaussian 03 Rev. B05, on Linux with Intel XEON 64-bit, without success. I have both PGI and IFC compilers. Can someone please give me some advice? 

Thank you in advance. 

P.S. : My search in the archive list has been not fruitful !!!!!!!!!!


Adlane
------=_Part_3642_30796383.1159267781878-- From owner-chemistry@ccl.net Tue Sep 26 16:10:00 2006 From: "Joseph Han jhh3851-,-yahoo.com" To: CCL Subject: CCL: Queue Systems for Linux PC Cluster Message-Id: <-32633-060926143255-12890-CGPFO8wZmGzeJLkDWbCDdg,,server.ccl.net> X-Original-From: Joseph Han Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 26 Sep 2006 10:32:48 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joseph Han [jhh3851###yahoo.com] There are third-party patches for OpenPBS which address the problems you describe. http://www.osc.edu/~troy/pbs/ http://www-unix.mcs.anl.gov/openpbs/ (Specifically the first two links under Patches to OpenPBS) With these patches, OpenPBS becomes much more usable. However, with that said, I think that today Torque is the better choice if considering OpenPBS. Joseph --- "Igor Filippov Contr igorf*_*helix.nih.gov" wrote: > Sent to CCL by: "Igor Filippov [Contr]" [igorf-.-helix.nih.gov] > On Tue, 2006-09-26 at 09:34, Karol Langner karol.langner/./kn.pl wrote: > > Sent to CCL by: Karol Langner [karol.langner!=!kn.pl] > > Hi list, > > > > On Tuesday 26 of September 2006 04:09, Fenglou Mao > fenglou+/-csbl.bmb.uga.edu > > wrote: > > > Sent to CCL by: "Fenglou Mao" [fenglou() csbl.bmb.uga.edu] > > > > > > We are using Sun Grid Engine, it is easy to install and easy to use, > > > compared with PBS, it is easier. One more important reason, in our system > > > PBS can only submit ~95% the jobs if you submit thousands of jobs by > using > > > script, but Sun Grid Engine can do all. > > What do you mean by this? Do you mean that PBS cannot submit certain types > of > > jobs, or that it can't handle such large queues? > > I believe PBS cannot handle large queues when a big number of jobs is > submitted _at_once_. > I have used OpenPBS and overall I cannot say that I would recommend it > to anyone - I was surprised to hear that many other people found it > otherwise. Perhaps they've been using the commercial fork - PBSpro, or > some non-standard version of OpenPBS, but stock OpenPBS leaves a lot to > be desired - problems with big job submissions are among the minor > issues compared to the rest. I've never used PBSpro, but considering the > open source version I'm not eager to try. > My topmost problem with OpenPBS is the way it handles failed nodes - if > a node is free, and for some reason - hardware problem etc. - it went > down, PBS marks it as being down and doesn't distribute jobs to that > node, everything as it should be. If, on the other hand, a node running > a job failed - the whole queuing system will get stuck, you won't be > able to submit a job, or check the status with qstat or even kill a job. > The only way out is either to restart the PBS or fix the failed node - > not the best way to have fault tolerance. > Add to that jobs getting stuck in exit status ("E"), jobs getting stuck > forever in queued status ("Q") and you might see that there are reasons > to consider alternatives to PBS. > > Regards, > Igor > > > > > Cheers, > > Karol> > > > From owner-chemistry@ccl.net Tue Sep 26 16:45:01 2006 From: "sabri alkis alkis . ufl.edu" To: CCL Subject: CCL: DLPOLY error mesage Message-Id: <-32634-060926152100-4158-xj9CACBxUADPNRf+xLdn3A=-=server.ccl.net> X-Original-From: "sabri alkis" Date: Tue, 26 Sep 2006 15:21:00 -0400 Sent to CCL by: "sabri alkis" [alkis*o*ufl.edu] Dear all, I have 6329 atoms(alkanthiol monolayer on gold surface and a silver cluster on top of these molecules) I used UFF(universal force field) parameters to calculate the vdw parameters between the atoms. When I run the simulation, I keep getting this error message "1-4 separation exceeds cutoff range". I tried different cutoff values but I got the same error message again.. I looked at the source code but I do not know why I got this message. What do u guys think the problem is? Is it wrong vdw parameters? What could I try? Best wishes Sab.. From owner-chemistry@ccl.net Tue Sep 26 18:00:00 2006 From: "Lukasz Cwiklik cwiklik]~[gmail.com" To: CCL Subject: CCL: polarisable force field for new molecule Message-Id: <-32635-060926102400-6891-/qLyeICe3aDVF4dJzKtFMg*|*server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 26 Sep 2006 13:29:22 +0000 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik\a/gmail.com] On 9/26/06, Bala Subramanian bala**igib.res.in wrote: > Sent to CCL by: "Bala Subramanian" [bala|*|igib.res.in] > Dear CCL users, > > I am working on nucleic acid-drug interaction. I am very new to this. I want to >use polarisable force field to simulate the complex. I can use ff02 for my DNA > in amber, but i dnt know how to generate polarisable ff for ligand or in general > any new molecule.Someone please suggest me on how i can do this. Hi, Not so long ago I was preparing polarizable force field parameters for simulations of small molecules in Amber. I found very useful the web page of Ulf Ryde: http://www.teokem.lu.se/~ulf/Methods/resp.html I have also prepared a tutorial how to do such a parametrization step by step. You can find it on my web page: http://www.molecular.cz/~cwiklik/publ.html (direct link: http://www.molecular.cz/~cwiklik/materials/resp_fitting.pdf) Best regards, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Tue Sep 26 21:27:00 2006 From: "Agalya agalya81-#-gmail.com" To: CCL Subject: CCL:G: HOMO-LUMO energy gap for cation radical Message-Id: <-32636-060926072551-6275-54DO3jncuE1sLWiNpsv0mg|server.ccl.net> X-Original-From: Agalya Content-Type: multipart/alternative; boundary="----=_Part_3082_2489322.1159269945624" Date: Tue, 26 Sep 2006 20:25:45 +0900 MIME-Version: 1.0 Sent to CCL by: Agalya [agalya81..gmail.com] ------=_Part_3082_2489322.1159269945624 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Sir, I am working on donor-acceptor polymers currently. So i wanted to study the properties of donor in its neutral, radical cation and dication state. And for acceptor in its neutral, radical anion and dication states. I have performed TDDFT for all these systems. For donor system, i have observed red shift in the spectrum going from neutral, cation radical and dicationic state. For acceptor systems, i observed anion radical shows red shift compared to dianion and neutral state. I wanted to analyse why this happens with the use of molecular orbital energy levels. Thankyou for your comments and suggestions. With Regards, Agalya On 9/26/06, Igor Avilov avilovi,averell.umh.ac.be wrote: > > Sent to CCL by: "Igor Avilov" [avilovi[a]averell.umh.ac.be] > Dear Agalya, > > It is indeed a question how to define the HOMO/LUMO gap for cation > radical. In the case when the molecule has a set of doubly occupied and > "fully" unoccupied orbitals, it is, of cause, clear how to do that. And then > the value of this HOMO/LUMO energy gap may be compared to, for example, the > lowest energy transition of the molecule. In the radical cation an electron > may be promoted, for example, from the singly-occupied orbital to some > unfilled orbital, or from some doubly occupied orbital (in the restricted > open shell treatment) to singly occupied orbital. Thus, if you are > interested in the excited states' properties it is better to perform, on my > opinion, TD-DFT calculation for your radical cation. So the question is: > what experimental data you want to explain? > > Best regards, > Igor. > > -----Original Message----- > > From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net] > Sent: dimanche 24 septembre 2006 14:59 > To: Igor Avilov > Subject: CCL:G: HOMO-LUMO energy gap for cation radical > > > Sent to CCL by: "Agalya G" [agalya81#%#gmail.com] > Dear CCL users, > > In my previous message i made typing mistakes. > > Kindly answer for this question. > > I have a querry regarding HOMO-LUMO gap for cation radical system. > > I have performed calculations for neutral, cation radical and dication > systems. > > 1) For neutral system, I used ( Charge=0 and spin multiplicity=1) > > 2) For cation radical system, I used ( Charge=+1 and spin multiplicity=2) > > 3) For dication, I used (charge=+2 and spin multiplicity=1) > > For neutal and dication systems, in gaussian03 program, it gives Occupied > and Virtual orbital energies with alpha spin. > > For cation radical system, it gives occupied and unoccupied orbital > energies for both alpha and beta spins. > > My querry is, how to compare HOMO-LUMO energy gaps between these systems. > > How to get HOMO-LUMO gap for cation radical system, in case i want to > compare this value with HOMO-LUMO energy gap with neutral and dication > systems. > > Kindly give me some suggestions. > > With Regards, > > Agalyahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > ------=_Part_3082_2489322.1159269945624 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Sir,

I am working on donor-acceptor polymers currently. So i wanted to study the properties of donor in its neutral, radical cation and dication state. And for acceptor in its neutral, radical anion and dication states.

I have performed TDDFT for all these systems. For donor system, i have observed red shift in the spectrum going from neutral, cation radical and dicationic state.

For acceptor systems, i observed anion radical shows red shift compared to dianion and neutral state. I wanted to analyse why this happens with the use of molecular orbital energy levels.

Thankyou for your comments and suggestions.

With Regards,
Agalya


On 9/26/06, Igor Avilov avilovi,averell.umh.ac.be <owner-chemistry .. ccl.net > wrote:
Sent to CCL by: "Igor Avilov" [avilovi[a]averell.umh.ac.be]
Dear Agalya,

It is indeed a question how to define the HOMO/LUMO gap for cation radical. In the case when the molecule has a set of doubly occupied and "fully" unoccupied orbitals, it is, of cause, clear how to do that. And then the value of this HOMO/LUMO energy gap may be compared to, for example, the lowest energy transition of the molecule. In the radical cation an electron may be promoted, for example, from the singly-occupied orbital to some unfilled orbital, or from some doubly occupied orbital (in the restricted open shell treatment) to singly occupied orbital. Thus, if you are interested in the excited states' properties it is better to perform, on my opinion, TD-DFT calculation for your radical cation. So the question is: what experimental data you want to explain?

Best regards,
Igor.

-----Original Message-----
> From: owner-chemistry^ccl.net [mailto:owner-chemistry^ccl.net]
Sent: dimanche 24 septembre 2006 14:59
To: Igor Avilov
Subject: CCL:G: HOMO-LUMO energy gap for cation radical


Sent to CCL by: "Agalya  G" [agalya81#%#gmail.com]
Dear CCL users,

In my previous message i made typing mistakes.

Kindly answer for this question.

I have a querry regarding HOMO-LUMO gap for cation radical system.

I have performed calculations for neutral, cation radical and dication systems.

1) For neutral system, I used ( Charge=0 and spin multiplicity=1)

2) For cation radical system, I used ( Charge=+1 and spin multiplicity=2)

3) For dication, I used (charge=+2 and spin multiplicity=1)

For neutal and dication systems, in gaussian03 program, it gives Occupied and Virtual orbital energies with alpha spin.

For cation radical system, it gives occupied and unoccupied orbital energies for both alpha and beta spins.

My querry is, how to compare HOMO-LUMO energy gaps between these systems.

How to get HOMO-LUMO gap for cation radical system, in case i want to compare this value with HOMO-LUMO energy gap with neutral and dication systems.

Kindly give me some suggestions.

With Regards,
Agalyahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt


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------=_Part_3082_2489322.1159269945624-- From owner-chemistry@ccl.net Tue Sep 26 22:02:00 2006 From: "Agalya G agalya81[A]gmail.com" To: CCL Subject: CCL: How to calculate Quantum yield Message-Id: <-32637-060926213213-24785-DSZ56GMLiu+QFOgXW8QZEg||server.ccl.net> X-Original-From: "Agalya G" Date: Tue, 26 Sep 2006 21:32:12 -0400 Sent to CCL by: "Agalya G" [agalya81###gmail.com] Dear CCL users, Can anyone explain me, how to calculate quantum yield or quantum efficiency? Thankyou in advance. With Regards, Agalya From owner-chemistry@ccl.net Tue Sep 26 22:57:01 2006 From: "Kalju Kahn kalju : chem.ucsb.edu" To: CCL Subject: CCL:G: Gaussian 03 and XEON 64-bit Message-Id: <-32638-060926180415-15056-XJqhZl2QNAfWPRksmtnE9g:server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Tue, 26 Sep 2006 15:04:09 -0700 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju|*|chem.ucsb.edu] Dear Adlane, I was not successful with versions earlier than D02 on Linux with Intel EM64T Nocona processor. Version D02 compiled fine with PGI 6.1 but not with PGI 6.2. Please let me know if you get it working with Intel compilers. Kalju ------------------- > Sent to CCL by: "Adlane sayede" [adlane.sayede^_^gmail.com] > ------=_Part_3642_30796383.1159267781878 > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > I am trying to compile Gaussian 03 Rev. B05, on Linux with Intel XEON > 64-bit, without success. I have both PGI and IFC compilers. Can > someone please give me some advice? > > Thank you in advance. > > P.S. : My search in the archive list has been not fruitful !!!!!!!!!! > > Adlane > > ------=_Part_3642_30796383.1159267781878 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: 7bit > Content-Disposition: inline > > 
I am trying to compile Gaussian 03 Rev. B05, on Linux with
Intel XEON 64-bit, without success. I have both PGI and IFC compilers.
Can someone please give me some advice? 

Thank you in advance.


P.S. : My search in the archive list has been not fruitful
!!!!!!!!!!
> 

Adlane
> > ------=_Part_3642_30796383.1159267781878--> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Tue Sep 26 23:42:00 2006 From: "Sidney Ramos Santana santanasidney%%yahoo.com.br" To: CCL Subject: CCL: DLPOLY error mesage Message-Id: <-32639-060926233909-11085-PFxl7IkLy+3yiAjOygUEsg ~~ server.ccl.net> X-Original-From: "Sidney Ramos Santana" Date: Tue, 26 Sep 2006 23:39:09 -0400 Sent to CCL by: "Sidney Ramos Santana" [santanasidney.:.yahoo.com.br] --- sabri alkis wrote -- > Data: Tue, 26 Sep 2006 16:49:20 -0400 > De: "sabri alkis alkis . ufl.edu" > Para: "Santana, Sidney Ramos -id4k3-" > Assunto: CCL: DLPOLY error mesage > Sent to CCL by: "sabri alkis" [alkis*o*ufl.edu] > Dear all, > > I have 6329 atoms(alkanthiol monolayer on gold surface and a silver > cluster on top of these molecules) I used UFF(universal force field) > parameters to calculate the vdw parameters between the atoms. When I run the > simulation, I keep getting this error message "1-4 separation exceeds > cutoff range". I tried different cutoff values but I got the same error > message again.. I looked at the source code but I do not know why I got > this message. What do u guys think the problem is? Is it wrong vdw > parameters? What could I try? > Best wishes > Sab.. -- Dear Sabri Alkis, Problably your simulations box is much bigger than it must be. Don't worry, this is normal! This usually happens when we want to simulate biological or organic system. I had a similar problem to simulate Biodiesel system with 11,000 atoms because the size of simulation box decreases while the simulation is runnning. My simulation box started with its box side equal to 90 angstroms and finished with 46 angstroms. Tips: 1) Let the volume to change !! So, Use NPT ensemble! 2) Problably, in your initial input, the CONFIG file, there is only the coordinates, and for a NPT simulation you also will need velocities and forces of the atoms. So, you must run a very small simulation using NVT ensemble, and in the end, you will get these properties. I would like to suggest some articles where you can undestand how the SPME Ewald works and how can we choose some parameter to get trustable and precise simulations. Please see: "How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines" J. Chem. Phys. 109 (1998) 7678 - 7693 "How to mesh up Ewald sums. II. An accurate error estimate for the particle-particle particle-mesh algorithm" J. Chem. Phys. 109 (1998) 7694 - 7701 3) Copy the last simulation box, in the REVCON file, to the CONFIG file and now, start a NPT long time simulations. Im my case I have been used 400,000 fs with a time step of 1 fs. 4) Repeate the Step 3) until the temperature and the pressure attain the room temperature and 1 atm, respectively. Warnings: If I understood well, you want to simulate a "gold surface". Well, computer simulations to describe surfaces only "make sense" if you employ a SLAB geometry in your periodic boundary conditions. But, when you do this the Ewald sum can not be used to calculate de long range interactions due some Ewald sum convergence problems in the reciprocal space that makes the calculation much more expensive computationally than its tre-dimensional counterpart. To more details, please see: Chapter 12.4 "Ewald Summation in a Slab Geometry" in "Understanding Molecular Simulation > From Algorithms to Applications" Daan Frenkel & Berend Smit 2nd Edition, Academic Press (2002) An alternative to this problem raise by the employment of a others methods, to calculate long range interactions as "Reaction Field". This method is implemented in the DLPOLY. Use the "chemometric" fit the dieletric constant for your system using, for example, the diffusion coefficient as a probe. Best regards, Sidney R. Santana Theoretical and Computational Chemistry Lab. (LQTC) Fundamental Chemistry Depart. (DQF) Federal University of Pernambuco (UFPE) Recife - PE - Brazil e-mail: santanasidney_at_yahoo.com.br