From owner-chemistry@ccl.net Wed Jun 10 03:11:01 2009 From: "andras.borosy[a]givaudan.com" To: CCL Subject: CCL: Application in idle time in a distributed Windows PC network (with 32 bit XPs)? Message-Id: <-39484-090609120927-7901-MpwXBd0KjV+GnmR/KE8sCw,+,server.ccl.net> X-Original-From: andras.borosy]~[givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0054FB5EC12575D0_=" Date: Tue, 9 Jun 2009 17:28:13 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy-$-givaudan.com This is a multipart message in MIME format. --=_alternative 0054FB5EC12575D0_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Do you know an application which is capable to generate COSMO files and=20 can be run in idle time in a distributed Windows PC network (with 32 bit=20 XPs)? Best regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 -=20 --=_alternative 0054FB5EC12575D0_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

Do you know an application which is capable to generate COSMO files and can be run in idle time in a distributed Windows PC network (with 32 bit XPs)?

Best regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -   --=_alternative 0054FB5EC12575D0_=-- From owner-chemistry@ccl.net Wed Jun 10 05:07:01 2009 From: "Syed Tarique Moin tarisyed]![yahoo.com" To: CCL Subject: CCL:G: Help in freezing the coordinates in a Gaussian input file. Message-Id: <-39485-090609131755-29982-0DlqCL3CwjWzN888pzCA4Q++server.ccl.net> X-Original-From: Syed Tarique Moin Content-Type: multipart/alternative; boundary="0-1106550410-1244564263=:94784" Date: Tue, 9 Jun 2009 09:17:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Syed Tarique Moin [tarisyed],[yahoo.com] --0-1106550410-1244564263=:94784 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Raj ks, First of all you have to made z-matrix of your system. Then those parameter= that you want to optimize should be accompanied with a word "variables". A= fter this put all parameters that you want to have constant (i.e. fixed of = frozen) should be accompanied by a word "constant".=20 The keyword in the route section should be opt=3Dz-matix.=20 a dummy input is given below -------------------------------------------------------------------- #opt=3Dz-matrix a =A0n=A0=A0 1 nfe2 =A0n=A0=A0 1 nfe3=A0=A0=A0=A0=A0=A0 2 nfen3 =A0n=A0=A0 1 nfe4=A0=A0=A0=A0=A0=A0 2 nfen4=A0=A0=A0=A0=A0=A0=A0 3 dih4 =A0n=A0=A0 1 nfe5=A0=A0=A0=A0=A0=A0 2 nfen5=A0=A0=A0=A0=A0=A0=A0 3 dih5 =A0o=A0=A0 1 ofe6=A0=A0=A0=A0=A0=A0 2 ofen6=A0=A0=A0=A0=A0=A0=A0 5 dih6 =A0o=A0=A0 6 oo7=A0=A0=A0=A0=A0=A0=A0 1 oofe7=A0=A0=A0=A0=A0=A0=A0 2 dih7 =A0c=A0=A0 2 cn8=A0=A0=A0=A0=A0=A0=A0 1 cnfe8=A0=A0=A0=A0=A0=A0=A0 6 dih8 =A0c=A0=A0 8 cc9=A0=A0=A0=A0=A0=A0=A0 2 ccn9=A0=A0=A0=A0=A0=A0=A0=A0 1 dih9 =A0n=A0=A0 9 nc10=A0=A0=A0=A0=A0=A0 8 ncc10=A0=A0=A0=A0=A0=A0=A0 2 dih10 =A0c=A0=A0 9 cc11=A0=A0=A0=A0=A0=A0 8 ccc11=A0=A0=A0=A0=A0=A0=A0 2 dih11 =A0=A0=A0=A0=A0 Variables: cn8=A0=A0=A0=A0=A0=A0=A0=A0 3.673079 cnfe8=A0=A0=A0=A0=A0=A0 159.551 =A0=A0=A0 Constants: nfe2=A0=A0=A0=A0=A0=A0=A0 2.196343 nfe3=A0=A0=A0=A0=A0=A0=A0 2.421082 -------------------------------------------------------------------- Regards Syed Tarique Moin --- On Tue, 6/9/09, raj s k cclselva]^[gmail.com = wrote: > From: raj s k cclselva]^[gmail.com Subject: CCL:G: Help in freezing the coordinates in a Gaussian input file. To: "Moin, Syed Tarique " Date: Tuesday, June 9, 2009, 4:04 AM Sent to CCL by: "raj s k" [cclselva^-^gmail.com] Hi, Can anyone explain (with the syntax) how to freeze the coordinates of a=20 few atoms in a model in Gaussian input file ? I have about 30 atoms in a=20 model and about 24 atoms have be frozen before an optimization process. It would be ideal if anyone can paste the text of an example Gaussian input= =20 file wherein few atomic coordinates are frozen. Thanks ks -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-1106550410-1244564263=:94784 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Raj ks,

First of all you have to = made z-matrix of your system. Then those parameter that you want to optimiz= e should be accompanied with a word "variables". After this put all paramet= ers that you want to have constant (i.e. fixed of frozen) should be accompa= nied by a word "constant".

The keyword in the route section should = be opt=3Dz-matix.
a dummy input is given below
---------------------= -----------------------------------------------
#opt=3Dz-matrix

a=
 n   1 nfe2
 n   1 nfe3  &nb= sp;    2 nfen3
 n   1 nfe4  &nbs= p;    2 nfen4        3 di= h4
 n   1 nfe5       2 nfen= 5        3 dih5
 o   1 ofe6       2 ofen6    &n= bsp;   5 dih6
 o   6 oo7    = ;    1 oofe7        2 dih= 7
 c   2 cn8        1 = cnfe8        6 dih8
 c &nbs= p; 8 cc9        2 ccn9   =       1 dih9
 n   9 nc10 &n= bsp;     8 ncc10      &nb= sp; 2 dih10
 c   9 cc11     &nbs= p; 8 ccc11        2 dih11
  = ;    Variables:
cn8      &n= bsp;  3.673079
cnfe8       159.551    Constants:
nfe2        2.196343
n= fe3        2.421082
-----------------= ---------------------------------------------------

Regards

<= br>Syed Tarique Moin



--- On Tue, 6/9/= 09, raj s k cclselva]^[gmail.com <owner-chemistry*ccl.net>= wrote:

From: raj s k cclselva]^[gmail.com = <owner-chemistry*ccl.net>
Subject: CCL:G: Help in freezing the coo= rdinates in a Gaussian input file.
To: "Moin, Syed Tarique " <= ;tarisyed*yahoo.com>
Date: Tuesday, June 9, 2009, 4:04 AM


Sent to CCL by: "raj s k" [cclselva^-^gmail.com]
Hi,
Can anyone explain (with the syntax) how = to freeze the coordinates of a
few atoms in a model in Gaussian input f= ile ? I have about 30 atoms in a
model and about 24 atoms have be froze= n before an optimization process.
It would be ideal if anyone can paste = the text of an example Gaussian input
file wherein few atomic coordinat= es are frozen.
Thanks
ks



-=3D This is automatically ad= ded to each message by the mailing script =3D-
To recover the email addr= ess of the author of the message, please change
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=0A= =0A --0-1106550410-1244564263=:94784-- From owner-chemistry@ccl.net Wed Jun 10 08:54:00 2009 From: "Daniel Kovich daniel.kovich],[gmail.com" To: CCL Subject: CCL: Computer touls Message-Id: <-39486-090610055129-17035-s1IX5cMDFZm75DtspiowMQ ~ server.ccl.net> X-Original-From: Daniel Kovich Content-Type: multipart/alternative; boundary=000e0cd1e2c48fbbea046bfaf938 Date: Wed, 10 Jun 2009 11:19:39 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Kovich [daniel.kovich/./gmail.com] --000e0cd1e2c48fbbea046bfaf938 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear all, Is there, in this forum, some one who is expert in fortran? I need some help to finalize the model of the Saccharomyces cerevisae's making. Thank you. Dr. Dan Univ Trieste Italy --000e0cd1e2c48fbbea046bfaf938 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear all,
Is there, in this forum, some one who is expert in fortran? I = need some help to finalize the model of the Saccharomyces cerevisae's m= aking.
=A0 Thank you.
Dr. Dan
Univ Trieste Italy
--000e0cd1e2c48fbbea046bfaf938-- From owner-chemistry@ccl.net Wed Jun 10 12:36:00 2009 From: "partha kundu partha1kundu^^^yahoo.com" To: CCL Subject: CCL: PED calculation Message-Id: <-39487-090610031634-32337-slb1eHxcP5Gleo4bsz58YA:-:server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary="0-1101383892-1244614557=:94436" Date: Tue, 9 Jun 2009 23:15:57 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu_._yahoo.com] --0-1101383892-1244614557=:94436 Content-Type: text/plain; charset=us-ascii Dear all, I want to do PED calculation. I tried in WinGAMESS by writting DECOMP=.TRUE in the force field. But in the output I could not find any result.Can any body help me in doing this with an example of a small molecule. Thanks in advance. regards. Partha --0-1101383892-1244614557=:94436 Content-Type: text/html; charset=us-ascii
Dear all,
I want to do PED calculation. I tried in WinGAMESS by writting DECOMP=.TRUE in the force field. But in the output I could not find any result.Can any body help me in doing this with an example of a small molecule.
Thanks in advance.
regards.
Partha

--0-1101383892-1244614557=:94436-- From owner-chemistry@ccl.net Wed Jun 10 14:58:00 2009 From: "Tapas Kar tapas.kar[A]usu.edu" To: CCL Subject: CCL: Vibrational scaling factor for UFF Message-Id: <-39488-090610144119-12403-IR5p/KVyuLxpZ7tDXTPpVQ * server.ccl.net> X-Original-From: "Tapas Kar" Date: Wed, 10 Jun 2009 14:41:16 -0400 Sent to CCL by: "Tapas Kar" [tapas.kar]^[usu.edu] Hello, I would appreciate reference on vibrational scaling factor for UFF method. Thanks Tapas From owner-chemistry@ccl.net Wed Jun 10 15:32:01 2009 From: "Tapas Kar tapas.kar---usu.edu" To: CCL Subject: CCL: Reference related to QM study of Ethambutol? Message-Id: <-39489-090610145036-13282-quo7FZ6FaL50Sd0rrjeG4Q{=}server.ccl.net> X-Original-From: "Tapas Kar" Date: Wed, 10 Jun 2009 14:50:32 -0400 Sent to CCL by: "Tapas Kar" [tapas.kar()usu.edu] Hello, I would appreciate theoretical (at the QM level) references on Ethambutol molecule. IUPAC name 2,2-(ethane-1,2-diyldiimino)dibutan-1-ol Thanks Tapas From owner-chemistry@ccl.net Wed Jun 10 16:07:01 2009 From: "Rajagopala Reddy Seelam rajagopalaseelam##gmail.com" To: CCL Subject: CCL: casscf convergence Message-Id: <-39490-090610135245-6900-cOBquQuQpXRLm9QpGhPTDQ^^server.ccl.net> X-Original-From: "Rajagopala Reddy Seelam" Date: Wed, 10 Jun 2009 13:52:41 -0400 Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam]|[gmail.com] Dear CCL members, I am doing CASSCF(9,9) calculations on a boron cluster having 7 boron atoms.I am calculating first excited state of that cluster.But my job is not converging even after 115 steps.That is not worrying me but the energy is diverging.B7 first excited state energy roughly around -172.53 hartrees.But it is now going towards -4603.54 hartrees.Is there any problem with my active space or it is only matter of convergence criteria.Below I am attaching input and output files. The input is as follows %mem= 1GB #p casscf(9,9,nroot=1) Symm=Loose aug-cc-pvdz scf(maxcyc=999) Distortion along normal mode N 4 by + 0.250 Q 0 2 5 0.000000 0.000000 0.323955 5 0.000000 1.651157 -0.058734 5 0.000000 -1.641000 -0.049251 5 -1.421148 0.820500 -0.049251 5 1.421148 0.820500 -0.049251 5 -1.429945 -0.825578 -0.058735 5 1.429945 -0.825578 -0.058735 9 10 11 this is the output last part ITN=115 MaxIt=999 E= -4601.8497836710 DE=-8.86D+00 Acc= 1.00D-05 Lan= 46 In Davids. NSec= 15876 IMaxHF,MaxMI,MSekIn,IFactt,WhenSc,nroot 50 50 2 2 2 1 ( 1) EIGENVALUE -0.46018498E+04 (12935) 0.4524283 (12942) 0.2738135 (12916)-0.2410506 (10793)-0.2217711 (12926)-0.2071529 (12053)-0.2017133 (12866) 0.1856483 ( 3863) 0.1688614 (10800)-0.1337897 (12939) 0.1335761 (12937) 0.1309124 (12923) 0.1260621 (12933) 0.1240924 (12060)-0.1221146 (12683) 0.1215589 (10774) 0.1170460 (12034) 0.1073143 ( 3870) 0.1020518 (10784) 0.1012536 (12873)-0.0956346 (13061) 0.0954179 (12976)-0.0940709 (12044) 0.0917943 (12936)-0.0911706 (10724)-0.0906121 ( 3844)-0.0896018 (11984)-0.0826550 ( 3854)-0.0771097 (12690) 0.0737561 ( 3794) 0.0688874 (12943) 0.0660326 (10797)-0.0659251 (12919)-0.0652508 (12664)-0.0649727 (10795)-0.0642637 (10289) 0.0626238 (10781)-0.0609129 (10791)-0.0604664 (12057)-0.0603525 (12055)-0.0587843 (12934) 0.0580989 (13068) 0.0576467 (12869) 0.0562419 (12041)-0.0559925 ( 3359)-0.0558323 (12674)-0.0558309 (12051)-0.0549995 (13042)-0.0506848 ( 3867) 0.0505400 (11801)-0.0505149 ( Davidson Disk Diagonalization is being used. max sub-space: 50 roots to seek: 1 dimension of matrix: 15876 Iteration 1 dimension is 1 Eigenvalues at current iteration: Root 1 : ******************** Iteration 2 dimension is 2 Root 1 not converged, maximum delta is 0.007594153503191 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.017422910342248 Iteration 3 dimension is 3 Root 1 not converged, maximum delta is 0.006752988738727 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.006945878778424 Iteration 4 dimension is 4 Root 1 not converged, maximum delta is 0.001344975762715 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000731570426069 Iteration 5 dimension is 5 Root 1 not converged, maximum delta is 0.001010286124652 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000304314563436 Iteration 6 dimension is 6 Root 1 not converged, maximum delta is 0.000428899449018 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000083170602920 Iteration 7 dimension is 7 Root 1 not converged, maximum delta is 0.001341970111254 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000137155263474 Iteration 8 dimension is 8 Root 1 not converged, maximum delta is 0.000812110815920 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000063421191953 Iteration 9 dimension is 9 Root 1 not converged, maximum delta is 0.000497200598114 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000030292202609 Iteration 10 dimension is 10 Root 1 not converged, maximum delta is 0.000345868860051 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000014611788174 Iteration 11 dimension is 11 Root 1 not converged, maximum delta is 0.000294075437948 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000010088069757 Iteration 12 dimension is 12 Root 1 not converged, maximum delta is 0.000159096398894 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000004757765964 Iteration 13 dimension is 13 Root 1 not converged, maximum delta is 0.000082851571797 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000002307770046 Iteration 14 dimension is 14 Root 1 not converged, maximum delta is 0.000033428283490 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000543217539 Iteration 15 dimension is 15 Root 1 not converged, maximum delta is 0.000076303251754 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000697692485 Iteration 16 dimension is 16 Root 1 not converged, maximum delta is 0.000082088507822 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000584279405 Iteration 17 dimension is 17 Root 1 not converged, maximum delta is 0.000100192712055 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000621482286 Iteration 18 dimension is 18 Root 1 not converged, maximum delta is 0.000038758043646 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000209155587 Iteration 19 dimension is 19 Root 1 not converged, maximum delta is 0.000035111857598 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000162335709 Iteration 20 dimension is 20 Root 1 not converged, maximum delta is 0.000023315090002 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000096487383 Iteration 21 dimension is 21 Root 1 not converged, maximum delta is 0.000012453466546 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000047000867 Iteration 22 dimension is 22 Root 1 not converged, maximum delta is 0.000017544503571 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000046834430 Iteration 23 dimension is 23 Root 1 not converged, maximum delta is 0.000013362193525 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000027689566 Iteration 24 dimension is 24 Root 1 not converged, maximum delta is 0.000006520976218 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000009799805 Iteration 25 dimension is 25 Root 1 not converged, maximum delta is 0.000005931520170 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000006053597 Iteration 26 dimension is 26 Root 1 not converged, maximum delta is 0.000007925408114 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000006612936 Iteration 27 dimension is 27 Root 1 not converged, maximum delta is 0.000005295919838 Eigenvalues at current iteration: Root 1 : ******************** Change is -0.000000003950845 Convergence achieved on expansion vectors. ibunc,ibunc2,ibuvec 641 640 23 Energy state 1 = -4603.5412571939 Full Convergence on CI vector WARNING! : large rotation I J = 100 14 Step scaled by 6.6655794573039673E-002 ITN=116 MaxIt=999 E= -4603.5412571939 DE=-1.69D+00 Acc= 1.00D-05 Lan= 27 Thank you for your kindness From owner-chemistry@ccl.net Wed Jun 10 16:43:00 2009 From: "arthur olson olson|-|scripps.edu" To: CCL Subject: CCL: Release of AutoDock Vina 1.0 Message-Id: <-39491-090609221149-29666-wQJL9HWpXDVsGfyOXRfi/w..server.ccl.net> X-Original-From: arthur olson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 Jun 2009 18:36:18 -0700 MIME-Version: 1.0 Sent to CCL by: arthur olson [olson|-|scripps.edu] Dear AutoDock users and others interested in receptor-ligand docking and virtual screening, Today we have concluded our beta test of AutoDock Vina and are announcing the first full release of AutoDock Vina 1.0 AutoDock Vina, a new docking code developed by Oleg Trott in my lab. AutoDock Vina uses the same format for the ligand and receptor files as AutoDock4, which can be prepared by AutoDock Tools, however its input is much simpler, and there is no need to run AutoGrid before runing the docking. The scoring and optimization procedures in AutoDock Vina are quite different than those in AutoDock4. A paper announcing and describing AutoDock Vina is now published online by the Journal of Computational Chemistry. http://www3.interscience.wiley.com/journal/122439542/abstract In the paper we compare its performance relative to AutoDock4. We have found AutoDock Vina is considerably faster than AutoDock4, with comparable or better docked structures for many complexes. AutoDock Vina 1.0 is distributed as binary executables for Linux and Windows and Mac platforms. It can be downloaded from http://vina.scripps.edu or via links from http://autodock.scripps.edu Changes from the previous beta version can be found at http://vina.scripps.edu/changes Thanks, Art Olson -- *************************************** Arthur J. Olson, Ph.D. Professor Department of Molecular Biology The Scripps Research Institute La Jolla, CA 92037 tel. (858) 784-9702 fax. (858) 784-2860 http://www.scripps.edu/pub/olson-web From owner-chemistry@ccl.net Wed Jun 10 19:33:00 2009 From: "Olexandr Isayev alex**ccmsi.us" To: CCL Subject: CCL: 9th Southern School on Computational Chemistry and Materials Science (Jackson, MS) Message-Id: <-39492-090610192237-6306-srxlf36j4ks5FWNxgT1EGA]![server.ccl.net> X-Original-From: Olexandr Isayev Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 Date: Wed, 10 Jun 2009 18:21:20 -0500 MIME-Version: 1.0 Sent to CCL by: Olexandr Isayev [alex]|[ccmsi.us] Dear Colleague On behalf of organizing committee I=92m pleased to inform you that 9th Southern School on Computational Chemistry and Materials Science will be held at the brand new Students Center of Jackson State University i= n Jackson, MS on July 28-29 (Tue and Wed), 2009. We are planning a small number of 40 minute lectures of invited speakers, 20 minute oral presentati= ons and posters. Meeting covers all areas of computational chemistry and materi= als science. For details on abstract and picture formats, conference program, online registration, and other information go through our conference web si= te: http://sscc.icnanotox.org Tentative list of invited speakers: David Close, East Tennessee State University Peter P. Fu, National Center for Toxicological Research, FDA Jayne Garno, Louisiana State University Philippe Guyot-Sionnest, University of Chicago Frances Hill, US Army ERDC Tobin J. Marks, Northwestern University Wujian Miao, The University of Southern Mississippi Jane Muray, University of New Orleans Peter Politzer, University of New Orleans B. Ramu Ramachandran, Louisiana Tech University Yinghong Sheng, Florida Gulf Coast University Andrzej Wierzbicki, University of South Alabama Looking forward to seeing you in Jackson Sincerely, Olexandr -- Olexandr Isayev, Ph D Department of Chemistry, Case Western Reserve University, Cleveland OH, 44106