From owner-chemistry@ccl.net Tue May 13 03:52:01 2008 From: "sobia ahsan halim sobia_halim],[yahoo.com" To: CCL Subject: CCL: Active site visualization software Message-Id: <-36942-080513034822-20142-vUj9ao/bmCOvsyPgPzfTGQ,,server.ccl.net> X-Original-From: "sobia ahsan halim" Date: Tue, 13 May 2008 03:48:18 -0400 Sent to CCL by: "sobia ahsan halim" [sobia_halim]-[yahoo.com] Dear All Hi Can any one kindly let me know about the free protein's active site characterization, building and visualizer software. Thanks. Bye. From owner-chemistry@ccl.net Tue May 13 05:50:01 2008 From: "Ariza Ahmad nriza|-|hotmail.com" To: CCL Subject: CCL: help on molecular charge distribution Message-Id: <-36943-080513054820-25308-8kYPQipGRdZwBT9ElcxU0A|,|server.ccl.net> X-Original-From: "Ariza Ahmad" Date: Tue, 13 May 2008 05:48:16 -0400 Sent to CCL by: "Ariza Ahmad" [nriza[]hotmail.com] Dear All, I have 1 questions that I don't understand well I read about charge distribution but I dont really understand the concept and explanation can somebody help me to explain in a simplify form? Regards Ariza From owner-chemistry@ccl.net Tue May 13 09:02:00 2008 From: "Herbert Fruchtl herbert.fruchtl * st-andrews.ac.uk" To: CCL Subject: CCL: How convert gamess orbitals to molpro orbitals Message-Id: <-36944-080513085213-1493-h/CxNDci0v+XlZe2X8CVug=-=server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 13 May 2008 13:51:39 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl%%st-andrews.ac.uk] The first problem in this seems to be that GAMESS prints its MOs in terms of Cartesian basis functions. Even if you use ISPHER=1, it will do the calculation with spherical harmonics (or at least give the same result as spherical harmonics would), but print the coefficients in terms of the Cartesian functions. Is there a way (short of writing a Fortran program...) to convert them to spherical harmonics? The rest should be straight-forward reformatting (except maybe the sequence question). Herbert Lilianna Bryjko lb435|a|st-andrews.ac.uk wrote: > Sent to CCL by: "Lilianna Bryjko" [lb435.*.st-andrews.ac.uk] > I'm looking for informations if there is any way to convert Gamess (US) orbitals to Molpro orbitals. Does maybe Gamess (US) have the option to print Molpro format orbitals. > > Lilianna Bryjko > University of St Andrews> > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Tue May 13 11:32:00 2008 From: "Antoine FORTUNE Antoine.Fortune---ujf-grenoble.fr" To: CCL Subject: CCL: AD4: ligand starting position Message-Id: <-36945-080513111510-12440-026wGHB4ObVExPEw18/13Q%a%server.ccl.net> X-Original-From: Antoine FORTUNE Content-Type: multipart/mixed; boundary="------------040504050603070907030709" Date: Tue, 13 May 2008 16:09:39 +0200 MIME-Version: 1.0 Sent to CCL by: Antoine FORTUNE [Antoine.Fortune\a/ujf-grenoble.fr] This is a multi-part message in MIME format. --------------040504050603070907030709 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Dear CCL'ers, dear Autodockers, Question(s) about Autodock4 : does ligand starting position impact docking results ? What appends if ligand coord. (ligand.pdbqt) are outside the gridbox ? ADT has a "User-Specified Initial Position : Random" check-box (preparing DPF with ADT) but produces a DPF with "move ligand.pdbqt about X Y Z", X Y Z not beeing random values but center of ligand in ligand.pdbqt file. I gess that check-box gives "tran0 random" and "quat0 random" but what is the range of that random ? Is it linked to tstep qstep and dstep and so limited to the vicinity of initial position (about 2A) or is it a random position anywhere in the gridbox ? Thank's for your lights ! AF --------------040504050603070907030709 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:;;Batiment E Pole Chimie - BP 53;GRENOBLE CEDEX 9;;38041;FRANCE email;internet:Antoine.Fortune---ujf-grenoble.fr title;quoted-printable:Ing=C3=A9nieur d'Etude Mod=C3=A9lisation Mol=C3=A9culaire tel;work:+33 4 76 63 52 92 x-mozilla-html:TRUE url:http://dpm.ujf-grenoble.fr version:2.1 end:vcard --------------040504050603070907030709-- From owner-chemistry@ccl.net Tue May 13 14:07:01 2008 From: "Nicola Salvi nicolasalvi _ email.it" To: CCL Subject: CCL: DL_POLY electric field Message-Id: <-36946-080513120336-30048-eOuOlcAI9abrEM7eJVwdhg#%#server.ccl.net> X-Original-From: "Nicola Salvi" Date: Tue, 13 May 2008 12:03:32 -0400 Sent to CCL by: "Nicola Salvi" [nicolasalvi{=}email.it] I have a problem with DL_POLY. I have to understand how to set up an external electric field in my simulation, parallel to z-axis. I know that I have to use elec command in FIELD file, but that's all I was able to find out, it still continues to output me error 52 and I didn't find much on web! Thanks all for your help! From owner-chemistry@ccl.net Tue May 13 14:44:01 2008 From: "YU XIAODI dee^xray.bmc.uu.se" To: CCL Subject: CCL: Problem about color when using Autodock Tool Message-Id: <-36947-080513101613-6440-DX3AaX60eHsf+zB3Ps0h8A{=}server.ccl.net> X-Original-From: YU XIAODI Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 13 May 2008 15:37:21 +0200 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: YU XIAODI [dee * xray.bmc.uu.se] Dear All: I have some problems about the colour when using ADT: 1), when I load the molecular, I can not colour them by Atom type directly. If I do like that, all the molecular will just turn black, the same as the background. Usually, I should first choose S&B and then I can colour them by Atom. 2), when I set the Grid box, the box which generated also became black, so I cannot see the box at all. If anyone face the same problem before? my computer is MacBook Pro, Mac OSX Version 10.4.11 Thanks a lot in advance, Dee From owner-chemistry@ccl.net Tue May 13 16:31:01 2008 From: "Aleksey Kuznetsov AlexKuznetsov2007|,|yandex.ru" To: CCL Subject: CCL: GAUSSIAN: "locking" the desired MO configuration when the 'guess=(read,alter)' command is used Message-Id: <-36948-080513163002-1730-EKT7UR9pzV3Aqt1aNgAwMg]*[server.ccl.net> X-Original-From: Aleksey Kuznetsov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 14 May 2008 00:29:43 +0400 MIME-Version: 1.0 Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007,+,yandex.ru] Dear CCL Users, I'm doing single-point calculations on the triplet system containing transition-metal dimer on TiO2 surface, at B3LYP/LanL2DZ level, with two alpha-orbitals transposed by 'guess=(read,alter)' command. I'd like to ask you for a piece of advice on this question: is there the effective way "to lock" the desired initial guess so that after finishing the single-point calculation I get exactly the state which I want, with two orbitals transposed? I ran the calculation with 'guess=(read,alter)' command using the 'vshift=N' (600 in my case) option, but the MO configuration returned to the original guess, and the orbitals did not get transposed. Thanks a lot! With best regards, Aleksey. ------------------------------------------- Dr. Aleksey Kuznetsov Cherry L. Emerson Center for Scientific Computation Emory University 1515 Dickey Drive Atlanta, GA 30322 USA Phone: (404)727-2381 Email: akuznets##euch4e.chem.emory.edu ------------------------------------------- From owner-chemistry@ccl.net Tue May 13 17:54:00 2008 From: "Reynier Suard az reynier.suardiaz]-[gmail.com" To: CCL Subject: CCL:G: NBO deletions prior to NJC procedure Message-Id: <-36949-080513172942-28936-pCLu+6gKjFDIg5igb/zJAQ===server.ccl.net> X-Original-From: "Reynier Suard az" Date: Tue, 13 May 2008 17:29:38 -0400 Sent to CCL by: "Reynier Suard az" [reynier.suardiaz-#-gmail.com] Dear all Does anybody know if it is possible to calculate the contribution of certain delocalization interaction to coupling constants in NBO5 using NBO deletions prior to NJC procedure? If this would be possible, I would like to know how an input file looks for NBO5.G in gaussian03. Thanks in advance reynier From owner-chemistry@ccl.net Tue May 13 18:29:01 2008 From: "Anastassia Alexandrova anastassia.alexandrova ~~ yale.edu" To: CCL Subject: CCL: GAUSSIAN: "locking" the desired MO configuration when the 'guess=(read,alter)' command is used Message-Id: <-36950-080513175214-32388-HxjZhPvHZpN2K99ziqu/lg . server.ccl.net> X-Original-From: Anastassia Alexandrova Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Tue, 13 May 2008 17:21:42 -0400 MIME-Version: 1.0 Sent to CCL by: Anastassia Alexandrova [anastassia.alexandrova#yale.edu] how about scf=qc? --------------------------------------- Anastassia Alexandrova, Ph.D. Yale University Department of Chemistry 225 Prospect Street New Haven, CT 06520-8107 Phone: 203-432-6288 Fax: 203-432-6144 anastassia.alexandrova/./yale.edu http://zarbi.chem.yale.edu/~anastassia/ --------------------------------------- Go one more mile... Quoting "Aleksey Kuznetsov AlexKuznetsov2007|,|yandex.ru" : > > Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007,+,yandex.ru] > Dear CCL Users, > > I'm doing single-point calculations on the triplet system containing > transition-metal dimer on TiO2 surface, at B3LYP/LanL2DZ level, with > two alpha-orbitals transposed by 'guess=(read,alter)' command. I'd > like to ask you for a piece of advice on this question: is there the > effective way "to lock" the desired initial guess so that after > finishing the single-point calculation I get exactly the state which > I want, with two orbitals transposed? I ran the calculation with > 'guess=(read,alter)' command using the 'vshift=N' (600 in my case) > option, but the MO configuration returned to the original guess, and > the orbitals did not get transposed. > > Thanks a lot! > > With best regards, > Aleksey. > ------------------------------------------- > Dr. Aleksey Kuznetsov > Cherry L. Emerson Center for Scientific Computation > Emory University > 1515 Dickey Drive > Atlanta, GA 30322 > USA > > Phone: (404)727-2381 > Email: akuznets .. euch4e.chem.emory.edu > -------------------------------------------> > From owner-chemistry@ccl.net Tue May 13 19:32:00 2008 From: "Jimmy Lawrence JLawrence(~)slb.com" To: CCL Subject: CCL: Newbie question on UV Vis calculation with GaussView Message-Id: <-36951-080513184741-32125-R5yhVjSN3QD3cGxMFS2cAA() server.ccl.net> X-Original-From: Jimmy Lawrence Content-language: en-US Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Wed, 14 May 2008 00:01:05 +0200 MIME-version: 1.0 Sent to CCL by: Jimmy Lawrence [JLawrence[a]slb.com] Dear CCL users, I have questions on calculating UV Vis spectra of the components that I have : Cd3S3H12 or Cd6S6H18 Optimization makes the structure weird, so I thought keeping the structure as they are defined in cif database would be the best. Can someone guide me with step-by-step procedure to obtain UV Vis spectra ? I tried ucis/lanl2dz scrf=(solvent=water) utd-hf but cannot get the spectra file (multiplicity error). Regards, Jimmy Lawrence From owner-chemistry@ccl.net Tue May 13 21:36:01 2008 From: "Brian Popp bvpopp*_*wisc.edu" To: CCL Subject: CCL: GAUSSIAN: "locking" the desired MO configuration when the 'guess=(read,alter)' command is used Message-Id: <-36952-080513212939-32700-qoS2PKvM62wnXfb7EgR8oQ=-=server.ccl.net> X-Original-From: Brian Popp Content-transfer-encoding: 7BIT Content-type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 13 May 2008 19:29:06 -0500 MIME-version: 1.0 Sent to CCL by: Brian Popp [bvpopp+*+wisc.edu] You might try iop(4/6=2) in addition to your standard input. This option turns off automatic basis projection that precedes the scf routine. However, this does not guarantee that your scf will converge to the desired electronic configuration. Good luck. -Brian ++++++++++++++++++++++++++ Dr. Brian V. Popp Postdoctoral Research Fellow Stahl Research Laboratory Department of Chemistry University of Wisconsin-Madison 1101 University Avenue Madison, WI 53066 Phone: (608) 265-8193 Fax: (608) 262-6143 ++++++++++++++++++++++++++ On May 13, 2008, at 4:21 PM, Anastassia Alexandrova anastassia.alexandrova ~~ yale.edu wrote: > > Sent to CCL by: Anastassia Alexandrova > [anastassia.alexandrova#yale.edu] > how about scf=qc? > --------------------------------------- > Anastassia Alexandrova, Ph.D. > Yale University > Department of Chemistry > 225 Prospect Street > New Haven, CT 06520-8107 > Phone: 203-432-6288 > Fax: 203-432-6144 > anastassia.alexandrova()yale.edu > http://zarbi.chem.yale.edu/~anastassia/ > --------------------------------------- > Go one more mile... > > > > Quoting "Aleksey Kuznetsov AlexKuznetsov2007|,|yandex.ru" > : > >> >> Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007,+,yandex.ru] >> Dear CCL Users, >> >> I'm doing single-point calculations on the triplet system >> containing transition-metal dimer on TiO2 surface, at B3LYP/LanL2DZ >> level, with two alpha-orbitals transposed by 'guess=(read,alter)' >> command. I'd like to ask you for a piece of advice on this >> question: is there the effective way "to lock" the desired initial >> guess so that after finishing the single-point calculation I get >> exactly the state which I want, with two orbitals transposed? I ran >> the calculation with 'guess=(read,alter)' command using the >> 'vshift=N' (600 in my case) option, but the MO configuration >> returned to the original guess, and the orbitals did not get >> transposed. >> >> Thanks a lot! >> >> With best regards, >> Aleksey. >> ------------------------------------------- >> Dr. Aleksey Kuznetsov >> Cherry L. Emerson Center for Scientific Computation >> Emory University >> 1515 Dickey Drive >> Atlanta, GA 30322 >> USA >> >> Phone: (404)727-2381 >> Email: akuznets .. euch4e.chem.emory.edu >> -------------------------------------------> >> > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > changehttp://www.ccl.net/chemistry/sub_unsub.shtml> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Tue May 13 22:20:01 2008 From: "John W Daily john.daily^^colorado.edu" To: CCL Subject: CCL: DL_POLY electric field Message-Id: <-36953-080513205556-18069-qShz1YcrWhzYeMTdX9eKRQ[*]server.ccl.net> X-Original-From: John W Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 13 May 2008 18:22:52 -0600 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: John W Daily [john.daily++colorado.edu] Nicola, You must have three lines. The following imposes an electric field of 5.0 (kcal units) in the x-dir. extern elec 5.0 0.0 0.0 And be sure to get the units right. They depend on the units you are using in the FIELD file. John On May 13, 2008, at 10:03 AM, Nicola Salvi nicolasalvi _ email.it wrote: > > Sent to CCL by: "Nicola Salvi" [nicolasalvi{=}email.it] > I have a problem with DL_POLY. I have to understand how to set up > an external electric field in my simulation, parallel to z-axis. I > know that I have to use elec command in FIELD file, but that's all > I was able to find out, it still continues to output me error 52 > and I didn't find much on web! > Thanks all for your help! > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > From owner-chemistry@ccl.net Tue May 13 22:55:00 2008 From: "Simon Halstead joyjoyhappyjoy|-|yahoo.co.uk" To: CCL Subject: CCL: DL_POLY electric field Message-Id: <-36954-080513222527-26489-9I4OrvW01sFjQY0hFNRuaQ/a\server.ccl.net> X-Original-From: Simon Halstead Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 13 May 2008 18:25:13 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Simon Halstead [joyjoyhappyjoy|-|yahoo.co.uk] Hi, Error 52 suggests that the FIELD file is not complete - it is expecting more information than you supply. Maybe if you post your full FIELD file we can see the problem. Also, there is a forum especially dedicated to dl_poly which may be of help in the future: http://www.cse.scitech.ac.uk/disco/forums/ubbthreads.php?ubb=postlist&Board=11&page=1 Goodluck, Simon --- "Nicola Salvi nicolasalvi _ email.it" wrote: > > Sent to CCL by: "Nicola Salvi" > [nicolasalvi{=}email.it] > I have a problem with DL_POLY. I have to understand > how to set up an external electric field in my > simulation, parallel to z-axis. I know that I have > to use elec command in FIELD file, but that's all I > was able to find out, it still continues to output > me error 52 and I didn't find much on web! > Thanks all for your help! > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the {} > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST{}ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/ > > > From owner-chemistry@ccl.net Tue May 13 23:30:01 2008 From: "Tapas Kar tapas.kar-.-usu.edu" To: CCL Subject: CCL:G: GAUSSIAN: "locking" the desired MO configuration when the 'guess=(read,alter)' command is used Message-Id: <-36955-080513195113-32028-IT5yU+aQlyxYptlx98PlNA|a|server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Tue, 13 May 2008 17:18:11 -0600 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar]=[usu.edu] Try SCF=3DSymm. -----Original Message----- > From: owner-chemistry+*+ccl.net [mailto:owner-chemistry+*+ccl.net] Sent: Tuesday, May 13, 2008 11:22 PM To: Tapas Kar Subject: CCL: GAUSSIAN: "locking" the desired MO configuration when the 'gu= ess=3D(read,alter)' command is used Sent to CCL by: Anastassia Alexandrova [anastassia.alexandrova#yale.edu] how about scf=3Dqc? --------------------------------------- Anastassia Alexandrova, Ph.D. Yale University Department of Chemistry 225 Prospect Street New Haven, CT 06520-8107 Phone: 203-432-6288 Fax: 203-432-6144 anastassia.alexandrova()yale.edu http://zarbi.chem.yale.edu/~anastassia/ --------------------------------------- Go one more mile... Quoting "Aleksey Kuznetsov AlexKuznetsov2007|,|yandex.ru" : > > Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007,+,yandex.ru] > Dear CCL Users, > > I'm doing single-point calculations on the triplet system containing > transition-metal dimer on TiO2 surface, at B3LYP/LanL2DZ level, with > two alpha-orbitals transposed by 'guess=3D(read,alter)' command. I'd > like to ask you for a piece of advice on this question: is there the > effective way "to lock" the desired initial guess so that after > finishing the single-point calculation I get exactly the state which > I want, with two orbitals transposed? I ran the calculation with > 'guess=3D(read,alter)' command using the 'vshift=3DN' (600 in my case) > option, but the MO configuration returned to the original guess, and > the orbitals did not get transposed. > > Thanks a lot! > > With best regards, > Aleksey. > ------------------------------------------- > Dr. Aleksey Kuznetsov > Cherry L. Emerson Center for Scientific Computation > Emory University > 1515 Dickey Drive > Atlanta, GA 30322 > USA > > Phone: (404)727-2381 > Email: akuznets .. euch4e.chem.emory.edu > -------------------------------------------> > -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt