From owner-chemistry@ccl.net Wed Jan 4 10:38:00 2006 From: "jaccob m chemjaccob+*+yahoo.co.in" To: CCL Subject: CCL: Calculations with heavy atoms Message-Id: <-30421-060104032020-13362-Po7VVrXiOm/fIOnJYe5r7w###server.ccl.net> X-Original-From: jaccob m Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1066851164-1136356377=:52150" Date: Wed, 4 Jan 2006 06:32:57 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: jaccob m [chemjaccob%x%yahoo.co.in] --0-1066851164-1136356377=:52150 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Thank you for your wishes. And also i wish you the same to all (Happy new year 2006). Sir you have to perform gas-phase calculations (thermochemistry) with compounds containing heavy atoms like Cesium. If we will do the gas-phase calculations (thermochemistry) with compounds containing heavy atoms like Cesium, what are the difficulities arises? So I request please send the details to me. I eagerly waiting for your answer. Thank you sir. "Florent Louis florent.louis(~)univ-lille1.fr" wrote: Sent to CCL by: "Florent Louis" [florent.louis]![univ-lille1.fr] Firstly, I wish all users an happy new year 2006. I have to perform gas-phase calculations (thermochemistry) with compounds containing heavy atoms like Cesium. What are the best methodologies (semi-empirical, ab initio, DFT, choice of the basis set or pseudopotential, treatment of the relativistic problem) and softwares ? I will be glad to receive any comments or feedback about it. Thanks, Sincerely Dr Florent LOUIShttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtSend instant messages to your online friends http://in.messenger.yahoo.com --0-1066851164-1136356377=:52150 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Thank you for your wishes. And also i wish you the same to all (Happy new year 2006). Sir you have to perform gas-phase calculations (thermochemistry) with compounds containing heavy atoms like Cesium. If we will do the gas-phase calculations (thermochemistry) with compounds containing heavy atoms like Cesium, what are the difficulities arises? So I request please send the details to me. I eagerly waiting for your answer.
                                      Thank you sir.

"Florent Louis florent.louis(~)univ-lille1.fr" <owner-chemistry]=[ccl.net> wrote:
Sent to CCL by: "Florent Louis" [florent.louis]![univ-lille1.fr]
Firstly, I wish all users an happy new year 2006. I have to perform gas-phase calculations (thermochemistry) with compounds containing heavy atoms like Cesium. What are the best methodologies (semi-empirical, ab initio, DFT, choice of the basis set or pseudopotential, treatment of the relativistic problem) and softwares ? I will be glad to receive any comments or feedback about it.
Thanks,
Sincerely
Dr Florent LOUIS






Send instant messages to your online friends http://in.messenger.yahoo.com --0-1066851164-1136356377=:52150-- From owner-chemistry@ccl.net Wed Jan 4 11:13:01 2006 From: "naga raja nagaraj_smart1984:-:yahoo.com" To: CCL Subject: CCL: clarification Message-Id: <-30422-060104053819-28946-0PXXPQNPcNqCtIq+T6tAPw]_[server.ccl.net> X-Original-From: naga raja Content-Transfer-Encoding: 8bit Content-Type: multipart/mixed; boundary="0-217365628-1136367492=:75911" Date: Wed, 4 Jan 2006 01:38:12 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: naga raja [nagaraj_smart1984|-|yahoo.com] --0-217365628-1136367492=:75911 Content-Type: multipart/alternative; boundary="0-146269936-1136367492=:75911" --0-146269936-1136367492=:75911 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Note: forwarded message attached. --------------------------------- Yahoo! Photos Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. --0-146269936-1136367492=:75911 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit



Note: forwarded message attached.

Yahoo! Photos
Ring in the New Year with Photo Calendars. Add photos, events, holidays, whatever. --0-146269936-1136367492=:75911-- --0-217365628-1136367492=:75911 Content-Type: message/rfc822 Content-Transfer-Encoding: 8bit Received: from [202.141.98.81] by web54002.mail.yahoo.com via HTTP; Sat, 31 Dec 2005 04:06:27 PST Date: Sat, 31 Dec 2005 04:06:27 -0800 (PST) > From: naga raja Subject: clarification To: amber^_^scripps.edu MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1471406782-1136030787=:44662" Content-Transfer-Encoding: 8bit Content-Length: 820 --0-1471406782-1136030787=:44662 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit respected sir/madam; i am from mk univesity in India.we r buying software amber8 have lot of douts are there . so u pls help me for these things. sir we are create a new pdb file and use XLEaP loading amber edit these these same pdb atoms are opened but bonds are not there .just simple porphyrin we r created errors display following contents FATAL: Atom .R .Adoes not have a type same above but the atom numberchanges continued .................. ................. .......... warning:close condact of 2.18 3717 angstroms between .R .A and .R.A 38 errors warning 42 u pls help me --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-1471406782-1136030787=:44662 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
respected sir/madam;
                 i am from mk univesity in India.we r buying software amber8 have lot of douts are there . so u pls help me for these things.
        sir we are create a new pdb file and use XLEaP loading amber edit these these same pdb atoms are opened but bonds are not there .just simple porphyrin we r created errors display following contents
FATAL: Atom .R<DEF 1> .A<c16 1>does not have a type
same above but the atom numberchanges continued
..................
.................
..........
warning:close condact of 2.18 3717 angstroms between .R <DEF 1 >.A <c16 1> and .R<DEF 1>.A<c15 2>
38 errors warning 42
u pls help me
 


Yahoo! Shopping
Find Great Deals on Holiday Gifts at Yahoo! Shopping --0-1471406782-1136030787=:44662-- --0-217365628-1136367492=:75911-- From owner-chemistry@ccl.net Wed Jan 4 12:27:00 2006 From: "Rick Venable rvenable*o*pollux.cber.nih.gov" To: CCL Subject: CCL: clarification Message-Id: <-30423-060104121724-9568-XSdmh3DlMr8UpzK6pPCMzA() server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 4 Jan 2006 12:13:18 -0500 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable!^!pollux.cber.nih.gov] For info and help with AMBER, try http://amber.scripps.edu/ ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- On Wed, 4 Jan 2006, naga raja nagaraj_smart1984:-:yahoo.com wrote: > respected sir/madam; > i am from mk univesity in India.we r buying > software amber8 have lot of douts are there . so u pls help > me for these things. sir we are create a new pdb file and > use XLEaP loading amber edit these these same pdb atoms are > opened but bonds are not there .just simple porphyrin we r > created errors display following contents > FATAL: Atom .R .Adoes not have a type > same above but the atom numberchanges continued > .................. > ................. > .......... > warning:close condact of 2.18 3717 angstroms between .R .A > and .R.A 38 errors warning 42 u pls help me From owner-chemistry@ccl.net Wed Jan 4 13:01:01 2006 From: "J.Aires de Sousa jas**fct.unl.pt" To: CCL Subject: CCL: MOPAC 7 and Fukui indices Message-Id: <-30424-060104121943-9899-QWK3VOPT87CDVAjjVg7Yjg_-_server.ccl.net> X-Original-From: "J.Aires de Sousa" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 04 Jan 2006 16:19:39 +0000 MIME-Version: 1.0 Sent to CCL by: "J.Aires de Sousa" [jas+/-fct.unl.pt] Dear CCL members I'd like some advice concerning the formulas for the calculation of Fukui reactivity indices from MOPAC 7 results (I know that recent commercial versions of MOPAC calculate Fukui indices). Could you comment on the different definitions of the Fukui indices? Can anyone tell me how to get the atomic contributions for >>>all<<< the molecular orbitals from MOPAC 7 without using the DEBUG keyword? -- Dr. Joao Aires de Sousa Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal Email: jas___at___fct.unl.pt From owner-chemistry@ccl.net Wed Jan 4 14:22:00 2006 From: "Nuno A.G. Bandeira nuno.bandeira .. ist.utl.pt" To: CCL Subject: CCL: MOPAC 7 and Fukui indices Message-Id: <-30425-060104142050-21465-PsReZYPjO/7w22f+5HAEcA_+_server.ccl.net> X-Original-From: "Nuno A.G. Bandeira" Sent to CCL by: "Nuno A.G. Bandeira" [nuno.bandeira{=}ist.utl.pt] J.Aires de Sousa jas**fct.unl.pt wrote: > Sent to CCL by: "J.Aires de Sousa" [jas+/-fct.unl.pt] > Dear CCL members > > I'd like some advice concerning the formulas for the calculation of > Fukui reactivity indices from MOPAC 7 results (I know that recent > commercial versions of MOPAC calculate Fukui indices). Could you comment > on the different definitions of the Fukui indices? As per Pearson's "Chemical Hardness" the Fukui function is the partial derivative of the electron density with respect to number of electrons (drho/dN). A practical form for the condensed Fukui function for electrophillic attack f(-) is: f(-) approx. equal to q(N) - q(N-1) for nucleophillic attack f(+) f(+) approx. equal to q(N+1)-q(N) Where q(N) is the charge of the individual atom in the species with N electrons. For the former and latter the definition can also be approximated by the square of the coefficient of the contribution of each atom in the HOMO and LUMO respectively. The atom with the highest Fukui function will be attacked by a soft electrophile/nucleophile but hard species will have their reaction controlled by electrostatics and will attack the most electronegative element in the molecule. An example would be thiocianate reacting with an electrophile for instance. The highest Fukui function is on sulphur but the most negative element (most negative charge) is nitrogen. Thus a soft electrophile will attack sulphur whereas the hard electrophile (such as H+) will attack nitrogen. Multiplying the global softness of the molecule by the Fukui index of an atom will by definition give you the local softness of that particular atom. regards, -- 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 Wed Jan 4 20:38:00 2006 From: "Grzegorz Bakalarski grzesb[a]biogeo.uw.edu.pl" To: CCL Subject: CCL:G: Gaussian compile on SUSE 10.0 Message-Id: <-30426-060104174254-4982-aaDUj9UZEfjEkzLElTdzkQ#server.ccl.net> X-Original-From: Grzegorz Bakalarski Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 4 Jan 2006 23:42:40 +0100 Mime-Version: 1.0 Sent to CCL by: Grzegorz Bakalarski [grzesb]_[biogeo.uw.edu.pl] Hi, I guess I know the problem... You need to look for errors (at least 2 or maybe 3) earlier in a compile log file. The problem is in gnu assembler. pgf77 compile to asembler code just fine but then assembler fails with stupid message (you'll find it in a log file). Optimization level has nothing to do (I tried -O0 - nothing better). Just gnu "as" for x86_64 fails. I've seen this situation on gentoo linux (x86_64) with kernel 2.6.11.8 or 2.6.15-rc4-current with GNU assembler version 2.16.1 (x86_64-pc-linux-gnu) using BFD version 2.16.1 I also tried PGI 5.2 and it fails also. But I could successfully compile on gentoo linux with kernel 2.6.11.11-current and GNU assembler version 2.15.92.0.2 (x86_64-pc-linux-gnu) using BFD version 2.15.92.0.2 20040927 Note 2.15.92.0.2 works and 2.16.1 does not. This has also nothing to SuSE itself (but I guess that SuSE 9 can have older version of assembler which may work). On my SuSE PIII (32-bit) machine I can compile just fine on SuSE 10 with: kernel 2.6.13-15.7-default and assembler: GNU assembler version 2.16.91.0.2 (i586-suse-linux) using BFD version 2.16.91.0.2 20050720 (SuSE Linux) I did not find other solution than to find a machine with other version of assembler .., Hope this helps Regards gb On Tue, Jan 03, 2006 at 12:44:49PM -0500, Grant Hill hilljg a cardiff.ac.uk wrote: > Sent to CCL by: Grant Hill [hilljg_-_cardiff.ac.uk] > Hi, > > First off, apologies to those who hate Gaussian support posts. > > I'm trying to compile Gaussian 03 (C02) on SUSE 10.0 with PGI 6 on a > EM64T xeon machine. The compile fails when it gets to building ml0.f > with the following error (snipped to get message size down): > > pgf77 -i8 '-mcmodel=medium' -mp -O2 -tp k8-64 -Mreentrant -Mrecursive > -Mnosave -Minfo -Mneginfo -time -fast -Munroll > -Mvect=assoc,recog,cachesize:1048576 -g -o g03 ml0.o > util.a /usr/lib/libgoto_prescott64p-r1.00.so -lm -lc > util.a(chain.o): In function `chain_': > chain.f:(.text+0x24f): undefined reference to `intowp_' > chain.f:(.text+0x2ad): undefined reference to `intowp_' > chain.f:(.text+0x527): undefined reference to `intowp_' > chain.f:(.text+0x5ba): undefined reference to `intowp_' > chain.f:(.text+0x92f): undefined reference to `ntstat_' > chain.f:(.text+0x9aa): undefined reference to `ntstat_' > chain.f:(.text+0xa25): undefined reference to `ntstat_' > chain.f:(.text+0xaa0): undefined reference to `ntstat_' > chain.f:(.text+0xabf): undefined reference to `ntrclo_' > chain.f:(.text+0xb1b): undefined reference to `ntstat_' > chain.f:(.text+0xb37): undefined reference to `ntrclo_' > util.a(fclose.o): In function `fclose_': > > I've changed the cachesize file to give the correct value, and pointed > at a different BLAS lib, but thats all that I have changed from the > default makefiles. Any ideas? > > Thanks in advance, > > Grant Hill> >