From owner-chemistry@ccl.net Fri Sep 15 00:05:01 2006 From: "Daniel Glossman-Mitnik daniel.glossman###cimav.edu.mx" To: CCL Subject: CCL:G: Gaussian input file for QST2 calculation Message-Id: <-32537-060915000308-28560-FTtaKQ2a6xfrUo7w0B13iA]|[server.ccl.net> X-Original-From: "Daniel Glossman-Mitnik" Date: Fri, 15 Sep 2006 00:03:07 -0400 Sent to CCL by: "Daniel Glossman-Mitnik" [daniel.glossman/a\cimav.edu.mx] Dear netters: I want to optimize the transition state for the reaction: C2H5* + C2H4 C4H9* (that is, ethyl radical + acetylene to give butyl radical) by using the QST2 facility in Gaussian 03. Can anybody help me by sending the Gaussian input file for this calculation ? Thanks in advance. Best regards, Daniel From owner-chemistry@ccl.net Fri Sep 15 01:11:00 2006 From: "Jan Labanowski janl(0)speakeasy.net" To: CCL Subject: CCL: NEWLEAD package for Linux and MAC OS X in CCL Archives Message-Id: <-32538-060915010744-32609-z5416we8AKZrGd2PVZhJXA-,-server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 15 Sep 2006 05:07:37 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl*|*speakeasy.net] I would like to thank Vincenzo Tschinke for a precious contribution to CCL Archives: the NEWLEAD package for Linux and Mac OS X (PPC): NEWLEAD is a computer program for the automatic generation of candidate structures. The input for the program is a set of fragments in the three-dimensional orientation corresponding to a given pharmacophore model. The treatment consists in connecting the fragments with spacers assembled from small chemical entities (atoms, chains or ring moieties). The results are new structures containing the fragments in the orientation defined in the input. The program offers the opportunity of rapidly applying a pharmacophore model in drug-design by generating automatically a set of chemical sructures conforming to the model. The package is available from: http://server.ccl.net/cca/software/MAC/newlead_linux_and_mac_osx/ The manual can be read on-line too... Thank you Vincenzo! Jan Labanowski CCL Manager jkl _ ccl.net From owner-chemistry@ccl.net Fri Sep 15 01:46:00 2006 From: "=?utf-8?B?RmFya2FzIMOWZMO2bg==?= farkas a chem.elte.hu" To: CCL Subject: CCL: Generate chiral forms Message-Id: <-32539-060914180821-3202-YrkNgAnrGlSa/OvR9Mp4KA%%server.ccl.net> X-Original-From: =?utf-8?B?RmFya2FzIMOWZMO2bg==?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Thu, 14 Sep 2006 22:54:35 +0200 MIME-Version: 1.0 Sent to CCL by: =?utf-8?B?RmFya2FzIMOWZMO2bg==?= [farkas]-[chem.elte.hu] Hi Manali, Chemaxon's Marvin is capable of that. It has a nice stereoisomer calculator plugin. Best wishes, Ödön Ödön Farkas Research associate professor Deparment of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas -----Original Message----- > From: owner-chemistry|,|ccl.net [mailto:owner-chemistry|,|ccl.net] Sent: Thursday, September 14, 2006 8:44 PM To: Farkas, XdXXn Subject: CCL: Generate chiral forms Sent to CCL by: "Manali Joshi" [manali*_*adrik.bchs.uh.edu] Hello, I wanted information about freeware to generate all possible chiral forms of a large set of small molecules in SMILES/MOL/MOL2 format. Any help would be greatly appreciated. Thanks in advance, Manalihttp://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 Fri Sep 15 02:42:00 2006 From: "Nehru Viji Shankaran chat2viji],[gmail.com" To: CCL Subject: CCL: internal to cartesian Message-Id: <-32540-060915015607-2991-o2me5X82r6JwgOxWqD42tA * server.ccl.net> X-Original-From: "Nehru Viji Shankaran" Date: Fri, 15 Sep 2006 01:56:06 -0400 Sent to CCL by: "Nehru Viji Shankaran" [chat2viji+/-gmail.com] Hi At present i'm working in computational chemistry. can anyone tell me the method to calculate the cartesian coordinates from the internal coordinates(z-matrix). thanks in advance, with regards, Nehru Viji shankaran. chat2viji/./gmail.com nehruviji/./yahoo.co.in From owner-chemistry@ccl.net Fri Sep 15 03:17:00 2006 From: "Dipankar Roy dipankarroy=iitb.ac.in" To: CCL Subject: CCL:G: Gaussian input file for QST2 calculation Message-Id: <-32541-060915021813-10906-wq4t3Fy4WEyGHqy+ML1qxg++server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 15 Sep 2006 10:48:07 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy!A!iitb.ac.in] Hi, QST2 input format is #ROUTE CARD(level of theory and basis set) OPT=QST2 FREQ Reactants C2H5* + C2H4 Charge Multiplicity coordinates of C2H5* + C2H4 Product Charge Multiplicity coordinates of C4H9* That is the standard input format. Please check the Gaussian user manual for more information. hope this will work. -Dipankar Roy > Sent to CCL by: "Daniel Glossman-Mitnik" [daniel.glossman/a\cimav.edu.mx] > Dear netters: > > I want to optimize the transition state for the reaction: > > C2H5* + C2H4 C4H9* > > (that is, ethyl radical + acetylene to give butyl radical) > > by using the QST2 facility in Gaussian 03. > > Can anybody help me by sending the Gaussian input file for this > calculation ? > > Thanks in advance. Best regards, > > Daniel> > > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratory Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) URL: http://www.geocities.com/dipankar_roy79/dipankar.html *********************************************** GETTING A SIMPLE ANSWER FROM A PROFESSOR IS LIKE GETTING A THIMBLE OF WATER FROM A FIRE HYDRANT. - PROF. LEN SHAPIRO, NDSU From owner-chemistry@ccl.net Fri Sep 15 06:37:00 2006 From: "Jens Thomas j.m.h.thomas-#-dl.ac.uk" To: CCL Subject: CCL: internal to cartesian Message-Id: <-32542-060915055751-25344-ffvouW64MN7TXm0qGrrflA|-|server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 15 Sep 2006 10:04:13 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas]_[dl.ac.uk] Hi Nehru, The CCP1GUI can convert between zmatrix and cartesian coordinates. You can find it at: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml Best wishes, Jens Nehru Viji Shankaran chat2viji],[gmail.com wrote: > Sent to CCL by: "Nehru Viji Shankaran" [chat2viji+/-gmail.com] > Hi > > At present i'm working in computational chemistry. > > can anyone tell me the method to calculate the cartesian coordinates from > > the internal coordinates(z-matrix). > > thanks in advance, > > with regards, > > Nehru Viji shankaran. > > chat2viji(_)gmail.com > nehruviji(_)yahoo.co.in> > > > > > From owner-chemistry@ccl.net Fri Sep 15 07:20:00 2006 From: "k.radacki k.radacki:+:mail.uni-wuerzburg.de" To: CCL Subject: CCL: implementation of visualization of SSCC pathways Message-Id: <-32543-060915044808-15476-E9O266xzYOANkHnwB4ppQg]^[server.ccl.net> X-Original-From: "k.radacki" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 15 Sep 2006 09:53:47 +0200 MIME-Version: 1.0 Sent to CCL by: "k.radacki" [k.radacki ~ mail.uni-wuerzburg.de] Reynier Suardiaz del Río reynier_-_fq.uh.cu wrote: > Sent to CCL by: =?iso-8859-1?Q?Reynier_Suardiaz_del_R=EDo?= [reynier!^!fq.uh.cu] > > Hi CCL > > Does somebody knows about a software that have implemented any kind of > visualization of nuclear spin - spin coupling pathways? as described in > > - O. Malkina and G. Malkin, Angew. Chem. Int. Ed. 2003, 42, 4335-4338 > - Martin Kaupp, Michael Bühl, Vladimir G. Malkin (Editors), Calculation of > NMR and EPR Parameters: Theory and Applications, Wiley-VCH Verlag GmbH & Co. > KGaA. Chapter 19. > > or any other...? > > Best regards > > reynier I'm to lazy to go two to 4th floor (you can write Martin if you want) but I believe that for visualization they use Molekel. mfg kris -- Dr. K. Radacki Institute of Inorganic Chemistry University of Wuerzburg D-97074 Germany From owner-chemistry@ccl.net Fri Sep 15 10:03:00 2006 From: "Bala subramanian bala%a%igib.res.in" To: CCL Subject: CCL: query on docking and SA calculation Message-Id: <-32544-060915095904-17382-DSZ56GMLiu+QFOgXW8QZEg-#-server.ccl.net> X-Original-From: "Bala subramanian" Date: Fri, 15 Sep 2006 09:59:03 -0400 Sent to CCL by: "Bala subramanian" [bala]|[igib.res.in] Dear CCl users, 1) I am using insightII affinity to do a docking.I face a problem of fixing solvation parameters for K+ ions in my structure. If i do the docking by removing the K+ ion from the strucutre, then it works, otherwise the docking doesnt work. I tried both grid docking and Simulated Annealing available with insightII, in both the cases this happens. Can anyone please suggest me how to fix this problem. 2) I want to calculate the solvent accessible area change of my DNA before and after docking with a ligand. Can someone suggest me any free and user friendly software available for this and also a software to calculate the thermodynamic parameters. thanks in advance, c.bala From owner-chemistry@ccl.net Fri Sep 15 11:11:00 2006 From: "Niharendu Choudhury nihcho * magnum.barc.gov.in" To: CCL Subject: CCL: DNA structure Message-Id: <-32545-060915021826-10962-iM9bJ+Tcx8fz3SgFPJj/4A#%#server.ccl.net> X-Original-From: Niharendu Choudhury Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 15 Sep 2006 10:47:02 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Niharendu Choudhury [nihcho]_[magnum.barc.gov.in] Is there any freeware by which one can generate PDB (coordinate) file of a DNA or modified DNA of one's choice of base pairs? I'll appreciate it very much if I get any information about it. Thanks Nihar ************************************************************************* * * * Dr. Niharendu Choudhury Tel: 91-22-2559 2675 * * Theoretical Chemistry Section, Fax: 91-22-2550 5151 * * RC & CD Division, Chemistry Group, 91-22-2551-9613 * * Mod. Lab, Email: nihcho ~ magnum.barc.ernet.in * * Trombay, Mumbai-400 085 * * INDIA * * * * Residence Tel. No. 91-22-2550 6261 * ************************************************************************* From owner-chemistry@ccl.net Fri Sep 15 11:49:00 2006 From: "Tapas Kar tapaskar]|[cc.usu.edu" To: CCL Subject: CCL: internal to cartesian Message-Id: <-32546-060915043102-14579-Foy99yWXeI5Dgco2QUWZUg.@.server.ccl.net> X-Original-From: "Tapas Kar" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 15 Sep 2006 01:44:59 -0600 MIME-Version: 1.0 Sent to CCL by: "Tapas Kar" [tapaskar*|*cc.usu.edu] Try Molden, Chem3d, Molekel -- Good Luck Tapas -----Original Message----- > From: owner-chemistry/./ccl.net [mailto:owner-chemistry/./ccl.net] Sent: Friday, September 15, 2006 12:47 AM To: Kar, Tapas Subject: CCL: internal to cartesian Sent to CCL by: "Nehru Viji Shankaran" [chat2viji+/-gmail.com] Hi At present i'm working in computational chemistry. can anyone tell me the method to calculate the cartesian coordinates from the internal coordinates(z-matrix). thanks in advance, with regards, Nehru Viji shankaran. chat2viji(_)gmail.com nehruviji(_)yahoo.co.inhttp://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 Fri Sep 15 12:23:01 2006 From: "Negi, Surendra S. ssnegi]_[utmb.edu" To: CCL Subject: CCL: DNA structure Message-Id: <-32547-060915112843-505-WS5oSwDEm5oVnQ30WBzhUw||server.ccl.net> X-Original-From: "Negi, Surendra S." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 15 Sep 2006 10:27:04 -0500 MIME-Version: 1.0 Sent to CCL by: "Negi, Surendra S." [ssnegi.#.utmb.edu] Try NAB from Scripps(David Case) Here is the link http://www.scripps.edu/mb/case/casegr-sh-3.2.html -----Original Message----- > From: Niharendu Choudhury nihcho * magnum.barc.gov.in [mailto:owner-chemistry#ccl.net] Sent: Fri 9/15/2006 10:15 AM To: Negi, Surendra S. Subject: CCL: DNA structure Sent to CCL by: Niharendu Choudhury [nihcho]_[magnum.barc.gov.in] Is there any freeware by which one can generate PDB (coordinate) file of a DNA or modified DNA of one's choice of base pairs? I'll appreciate it very much if I get any information about it. Thanks Nihar ************************************************************************* * * * Dr. Niharendu Choudhury Tel: 91-22-2559 2675 * * Theoretical Chemistry Section, Fax: 91-22-2550 5151 * * RC & CD Division, Chemistry Group, 91-22-2551-9613 * * Mod. Lab, Email: nihcho/./magnum.barc.ernet.in * * Trombay, Mumbai-400 085 * * INDIA * * * * Residence Tel. No. 91-22-2550 6261 * *************************************************************************http://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 Fri Sep 15 12:58:01 2006 From: "Mehmed Zahid Ertem mzertem(a)gmail.com" To: CCL Subject: CCL:G: Microiterations in ONIOM Message-Id: <-32548-060915122654-29396-klLzgQ8t/R86nwJL4UpC3w . server.ccl.net> X-Original-From: "Mehmed Zahid Ertem" Date: Fri, 15 Sep 2006 12:26:54 -0400 Sent to CCL by: "Mehmed Zahid Ertem" [mzertem%x%gmail.com] Dear CCLers, I want to share a problem that I came across during my QMMM optimizations using ONIOM keyword implemented in G03. I don't know whether I made a mistake or the thing I'm asking is not possible. I have done geometry optimizations by using: ONIOM(B3LYP/3-21G*:AMBER=softfirst)=embedcharge opt=gdiis and observed the microiterations in the .log file. After these optimizations I tried to find a transition state by using: ONIOM(B3LYP/3-21G*:AMBER=softfirst)=embedcharge opt=(ts,noeigen,gdiis,modredundant) but faced with a extremely slower advance in computations and also noticed that microiterations were not presented in the .log file. Can this (the absence of microiterations) be the reason for increased time of calculation or am I missing something? Thank you in advance, Mehmed Zahid ERTEM Bogazici University Chemistry Department MS Student From owner-chemistry@ccl.net Fri Sep 15 13:50:00 2006 From: "SANDEEP KUMAR kumarsan%x%jhu.edu" To: CCL Subject: CCL: DNA structure Message-Id: <-32549-060915134756-4231-Dy0/7pHDBl3hjPfcYX3OsA+/-server.ccl.net> X-Original-From: SANDEEP KUMAR Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Fri, 15 Sep 2006 12:47:48 -0400 MIME-version: 1.0 Sent to CCL by: SANDEEP KUMAR [kumarsan(-)jhu.edu] Dr. Nihar: Please contact Prof. Bansal at IISc. Her lab has developed NUCGEN and NUPARM programs for generation and analysis of Nucleic acid structures in 1990's. Sincerely, Sandeep ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan^jhu.edu. URL: https://jshare.johnshopkins.edu/skumar23/public_html/ Previous URL: http://www.lecb.ncifcrf.gov/~kumarsan ----- Original Message ----- > From: "Niharendu Choudhury nihcho * magnum.barc.gov.in" Date: Friday, September 15, 2006 11:21 am Subject: CCL: DNA structure To: "Kumar, Sandeep " > Sent to CCL by: Niharendu Choudhury [nihcho]_[magnum.barc.gov.in] > Is there any freeware by which one can generate PDB (coordinate) > file of a > DNA or modified DNA of one's choice of base pairs? > > I'll appreciate it very much if I get any information about it. > Thanks > > Nihar > > > > ************************************************************************* * * > * Dr. Niharendu Choudhury Tel: 91-22-2559 2675 > * > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 > * > * RC & CD Division, Chemistry Group, 91-22-2551-9613 > * > * Mod. Lab, Email: > nihcho/./magnum.barc.ernet.in * > * Trombay, Mumbai-400 085 > * > * INDIA > * > * > * > * Residence Tel. No. 91-22-2550 6261 > * > > ************************************************************************* > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the ^ sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Fri Sep 15 14:24:00 2006 From: "huanglei huanglei!=!mail.utexas.edu" To: CCL Subject: CCL: DNA structure Message-Id: <-32550-060915134121-3926-RuevA3fbAOXR1V3c5MO9Hg,server.ccl.net> X-Original-From: "huanglei" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="gb2312" Date: Fri, 15 Sep 2006 11:20:59 -0500 Mime-Version: 1.0 Sent to CCL by: "huanglei" [huanglei|,|mail.utexas.edu] You can try NUCLEIC in Tinker, a free package at http://dasher.wustl.edu/tinker/. Good luck! Best regards, lei ======= 2006-09-15 10:14:41 ======= >Sent to CCL by: Niharendu Choudhury [nihcho]_[magnum.barc.gov.in] >Is there any freeware by which one can generate PDB (coordinate) file of a >DNA or modified DNA of one's choice of base pairs? > >I'll appreciate it very much if I get any information about it. >Thanks > >Nihar > > > ************************************************************************* > * * > * Dr. Niharendu Choudhury Tel: 91-22-2559 2675 * > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 * > * RC & CD Division, Chemistry Group, 91-22-2551-9613 * > * Mod. Lab, Email: nihcho/./magnum.barc.ernet.in * > * Trombay, Mumbai-400 085 * > * INDIA * > * * > * Residence Tel. No. 91-22-2550 6261 * > *************************************************************************> > = = = = = = = = = = = = = = = = = = = = Best regards, ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡huanglei ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡huanglei . mail.utexas.edu ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-09-15 From owner-chemistry@ccl.net Fri Sep 15 15:56:01 2006 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas(a)chem.elte.hu" To: CCL Subject: CCL:G: Microiterations in ONIOM Message-Id: <-32551-060915154505-4833-hfbQIQA7ww8bXQiv1u9l6Q~!~server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 15 Sep 2006 20:42:08 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas _ chem.elte.hu] Hi Mehmed, Try Opt=(Mic120,...). I guess TS or ModRedundant turned off the otherwise automatic microiterations. Good luck! Odon On Fri, 2006-09-15 at 13:00 -0400, Mehmed Zahid Ertem mzertem(a)gmail.com wrote: > Sent to CCL by: "Mehmed Zahid Ertem" [mzertem%x%gmail.com] > Dear CCLers, > > I want to share a problem that I came across during my QMMM optimizations using ONIOM keyword implemented in G03. I don't know whether I made a mistake or the thing I'm asking is not possible. > > I have done geometry optimizations by using: > > ONIOM(B3LYP/3-21G*:AMBER=softfirst)=embedcharge opt=gdiis > > and observed the microiterations in the .log file. After these optimizations I tried to find a transition state by using: > > ONIOM(B3LYP/3-21G*:AMBER=softfirst)=embedcharge opt=(ts,noeigen,gdiis,modredundant) > > but faced with a extremely slower advance in computations and also noticed that microiterations were not presented in the .log file. Can this (the absence of microiterations) be the reason for increased time of calculation or am I missing something? > > Thank you in advance, > > Mehmed Zahid ERTEM > Bogazici University > Chemistry Department > MS Student> > > -- Ödön Farkas Research associate professor Deparment of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Fri Sep 15 16:31:00 2006 From: "Debasis Sengupta dxs:-:cfdrc.com" To: CCL Subject: CCL:G: G03W Multiprocessor experience? Message-Id: <-32552-060915142909-16162-mfz0FcwEvghhJ6438YYXrw!^!server.ccl.net> X-Original-From: Debasis Sengupta Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 15 Sep 2006 11:58:27 -0500 MIME-Version: 1.0 Sent to CCL by: Debasis Sengupta [dxs-,-cfdrc.com] Hi Has anybody bought G03W multiprocessor version? Wanted to know how good it is. debasis From owner-chemistry@ccl.net Fri Sep 15 20:09:00 2006 From: "David A. Case case{=}scripps.edu" To: CCL Subject: CCL: Mopac on Linux using g77 Message-Id: <-32553-060915192830-11662-fSfG2QvFy/lvDJnqLzkWdA_+_server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 15 Sep 2006 13:43:41 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case|-|scripps.edu] On Thu, Sep 14, 2006, Rick Muller rpmuller{=}gmail.com wrote: > I'm having all kinds of difficulties getting mopac7 to work on linux using > g77. I simply cannot get the test cases to work properly. Has anyone gotten > this to work? If so, did you have to do anything special to make it work? The usual advice is to add the flags "-fno-automatic -finit-local-zero" to your compiler flags. Mostly, the mopac{5,6,7} codes were written for compilers that did this sort of thing by default, but now you have to specify it explicitly. I can't guarantee that this will work for you, but it is simple enough to certainly be worth a try. (I'm pretty sure that this is all that needs to be done to get mopac6 to work, so I hope it will work for mopac7 as well.) If you still have troubles, you can download the antechamber codes from http://amber.scripps.edu/antechamber. This package contains a version of mopac6 that has worked pretty well for us. ...good luck...dave case From owner-chemistry@ccl.net Fri Sep 15 20:44:00 2006 From: "elainerchan elainerchan,gmail.com" To: CCL Subject: CCL: DNA structure Message-Id: <-32554-060915160252-15752-sR7aJxqWE69zAeRO9RrZnw###server.ccl.net> X-Original-From: elainerchan Content-Type: multipart/alternative; boundary="----=_Part_116989_2563870.1158348263552" Date: Fri, 15 Sep 2006 12:24:23 -0700 MIME-Version: 1.0 Sent to CCL by: elainerchan [elainerchan/a\gmail.com] ------=_Part_116989_2563870.1158348263552 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline See the publication: E. R. Chan, ICCAR: Fortran Program to Convert Internal Coordinates to Cartesian Coordinates, IBM Technical Report (1975)RJ1594(#23718)public ~%~%~%~%~%%~%%~%%%~%~%~%~%~%~%%~%~%%%~!%~%~%~% On 9/15/06, Niharendu Choudhury nihcho * magnum.barc.gov.in < owner-chemistry-.-ccl.net> wrote: > > Sent to CCL by: Niharendu Choudhury [nihcho]_[magnum.barc.gov.in] > Is there any freeware by which one can generate PDB (coordinate) file of a > DNA or modified DNA of one's choice of base pairs? > > I'll appreciate it very much if I get any information about it. > Thanks > > Nihar > > > ************************************************************************* > * * > * Dr. Niharendu Choudhury Tel: 91-22-2559 2675 * > * Theoretical Chemistry Section, Fax: 91-22-2550 5151 * > * RC & CD Division, Chemistry Group, 91-22-2551-9613 * > * Mod. Lab, Email: nihcho/./magnum.barc.ernet.in > * > * Trombay, Mumbai-400 085 * > * INDIA * > * * > * Residence Tel. No. 91-22-2550 6261 * > *************************************************************************> > > > -- %~%~%~%~%~%~%~%~%~%~%~%~%~% ------=_Part_116989_2563870.1158348263552 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
See the publication:

E. R. Chan, ICCAR: Fortran Program to Convert Internal Coordinates to Cartesian Coordinates, IBM Technical Report (1975)RJ1594(#23718)public


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On 9/15/06, Niharendu Choudhury nihcho * magn= um.barc.gov.in <owner= -chemistry-.-ccl.net > wrote:
Sent to CCL by: Niharendu Choudhury [nihcho]_[ magnum.barc.gov.in]
Is there any freeware by which one can generate = PDB (coordinate) file of a
DNA or modified DNA of one's choice of base p= airs?

I'll appreciate it very much if I get any information about it= .
Thanks

Nihar


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