From chemistry-request@server.ccl.net Wed Dec 15 01:58:18 1999 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA17326 for ; Wed, 15 Dec 1999 01:58:13 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id LAA00528 for ; Wed, 15 Dec 1999 11:10:00 +0530 Received: from localhost (tcg@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) with SMTP id LAA07469 for ; Wed, 15 Dec 1999 11:37:20 +0530 Date: Wed, 15 Dec 1999 11:37:19 +0530 (IST) From: "Students of Dr. S.R. Gadre" Reply-To: "Students of Dr. S.R. Gadre" To: CHEMISTRY@server.ccl.net Subject: Any Review one solvation? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sirs/Madams: We are currently interested in studying hydration patterns of some small and medium, biologically intersting molecules. Is there any review on structure making and structure breaking (thermodynamic) properties molecules? Any help would be appreciated. Babu. k From chemistry-request@server.ccl.net Wed Dec 15 07:58:31 1999 Received: from dalton.quimica.unlp.edu.ar (root@dalton.quimica.unlp.edu.ar [163.10.18.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA19541 for ; Wed, 15 Dec 1999 07:58:29 -0500 Received: from bilbo (jubert4.quimica.unlp.edu.ar [163.10.18.18]) by dalton.quimica.unlp.edu.ar (8.9.0/8.9.0) with SMTP id IAA16455 for ; Wed, 15 Dec 1999 08:28:06 -0300 Message-Id: <3.0.1.32.19991215084631.00693290@dalton.quimica.unlp.edu.ar> X-Sender: pis_diez@dalton.quimica.unlp.edu.ar X-Mailer: Windows Eudora Light Version 3.0.1 (32) Date: Wed, 15 Dec 1999 08:46:31 -0300 To: chemistry@ccl.net From: Reinaldo Pis Diez Subject: Re: CCL:ZINDO MO coeffs in G98 -> summary Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi netters, Yesterday (!) I asked the net about > Is there any way to print the MO coeffs in the output for a Zindo/S job > in G98? Jens Antony gave me the hint: the internal option iop(5/33=2) must be used instead of iop(6/7=3) as one expected to get molden inputs. I want to add also that using iop(5/33=1) doesn't work. This internal option states that "The eigenvalues and the MO coeffs are printed at the end of the SCF" according to G98 Progammer's Reference, page 111. Thanks Jens!! Regards, Reinaldo Dear Reinaldo! Try IOp(5/33=2). Regards, Jens From chemistry-request@server.ccl.net Tue Dec 14 12:46:32 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA13847 for ; Tue, 14 Dec 1999 12:46:31 -0500 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id LAA09692 for ; Tue, 14 Dec 1999 11:35:57 -0500 (EST) Sender: desingh@mailbox.syr.edu Message-ID: <3856730C.E18E4BE0@syr.edu> Date: Tue, 14 Dec 1999 11:40:44 -0500 From: Deepak Singh Organization: Dept. of Chemistry, Syracuse University X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: Visualizing orbitals Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here is the text from a post I made a while ago. Sorry for the delay in this message but I was trying out a few options. ---------------------------------------- Hi, I have been looking into software (for IRIX) that will allow me to visualize MO's, charge densities etc. I heard a lot about AVS but that seems to have disappeared. I ran into IBM's 'Open Visualization Data Explorer' today and it seems to be similar to AVS. I would like to know if people have used this a lot with G98/94, GAMESS and MOPAC? Is the performance similar to AVS? Thanks Deepak ------------------------------------------- I got a lot of replies. Amongst other things, I was told that AVS still exists as AVS Express. Here is a post that covers AVS Express/IBM Explorer -------------------------------------------------------- Hi Deepak, AVS the company still exists (www.avs.com), and AVS the package (AVS5) has been reincarnated as Viz Express. I have used it to visualize charge densities and other spatial fields with some success (see my web page for an old example of delta-rho at a defect in a grain boundary). However I found it limited in other ways-- volume rendering for example. AVS is proprietary and costs ~ $1000/copy (I run it on an SGI Indigo-2). I have been thinking about trying Data Explorer-- I know a number of people who have used it for chemistry applications and have been very happy with it. Also the price is right (free). There is some history about AVS and Data Explorer-- one broke off from the other-- they used to be part of the same product-- but I don't recall the details. IBM's Data Explorer used to be proprietary but it recently went 'open'. Regarding performance-- I have no idea, but I suspect that the bottom line will be the quality of your workstation's graphics board (I have an SGI Indigo2 High Impact/R10000/195 MHz and AVS runs very well with that). I have also just returned from Supercomputing '99 and saw a demo of a new visualization package, Amira, which was used to do some fantastic volume rendering of scalar fields (for an astrophysics application, but it would seem very applicable to visualizing molecular orbitals)-- check out http://www.amiravis.com or www.tgs.com. I am planning to do this myself :-) Cheers, Susan ----------------------------------------------------------- After looking at the IBM product and some other suggestions, I decided that for the price and effort the best out there are still MOLDEN and MOLEKEL. The latter which I had never used is excellent for use with Gaussian and GAMESS. MOLDEN's vrml pictures are great too. I still would like to spend more time with IBM explorer as the pictures are very pretty but at a later date MOLDEN is available at http://www.caos.kun.nl/~schaft/molden/molden.html and MOLEKEL (only for SGI's) at http://igc.ethz.ch/molekel/ Thanks to everyone who replied Regards Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Tue Dec 14 13:23:45 1999 Received: from beryllium.camsoft.com (beryllium.camsoft.com [198.112.109.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA14049 for ; Tue, 14 Dec 1999 13:23:45 -0500 Message-Id: <199912141823.NAA14049@server.ccl.net> Received: from 198.112.109.100 by beryllium.camsoft.com with SMTP (QuickMail Pro Server for MacOS 1.0.3); 14 DEC 99 12:14:23 UT Date: 14 Dec 99 12:09:30 -0500 From: Kam Chana Subject: RE: CCL:Electrostatic potential surface with G98/Chem3D To: chemistry X-Mailer: QuickMail Pro 1.5.2 (Mac) X-Priority: 3 MIME-Version: 1.0 Reply-To: Kam Chana Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id NAA14050 RE: CCL:Electrostatic potential surface wi 12/14/99 Dear Dr. Kincaid, Please contact me or our support to help you resolve this problem. The error that Chem3D is generating is because the data in cube file will not allow Chem3D to generate a reasonable iso-potential surface. Sincerely, Kam Chana, Ph.D ksc@camsoft.com CambridgeSoft Corporation. -- À̼º±¤ wrote: >Dear Dr. Kincaid, > >I recommand you to use gOpenmol program. >This program diplay ESP surface using plt format recognized >by gOpenMol that tranferred from G98w cube file. >In detail, See as follows. > >http://laaksonen.csc.fi/gopenmol/gopenmol.html >http://laaksonen.csc.fi/gopenmol/utility.html > >-------------------------------------------------------------- >Sung Kwang Lee Ph. D Student Analytical Chemistry > >E-mail lsk@alchemy.yonsei.ac.kr >Address Dept.of Chem., Yonsei Univ. Seoul, 120-749, S. Korea >Tel 82-2-361-2635 Fax 82-2-364-7050 >WWW http://chem.yonsei.ac.kr/~lsk/ , http://www.qspr.pe.kr >-------------------------------------------------------------- > > >> Hello, >> >> Lately I've been trying to generate the electrostatic potential of >> organometallic compounds using G98W and Chem3D, however, anytime I try and >> generate the ESP surface using Chem3D from the formatted checkpoint file it >> says there is an error in the file (it generates the orbitals no trouble). >> I've tried generating the cube file directly (cube=potential, prop) but when I >> try and read this into chem3d it gives a warning that the density is very low >> and doesn't display the ESP surface. >> >> Any ideas? >> >> Thanks in advance, >> >> Kevin Kincaid. >> >> ____________ >> >> Kevin Kincaid >> chemistry.forums@usa.net >> Dublin City University, Ireland > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > >RFC822 header >----------------------------------- > >RECEIVED: from SF_Database by POP_Mailbox_-1266952729 ; 14 DEC 99 11:09:27 >UT >Received: from SERVER.CCL.NET by beryllium.camsoft.com > with SMTP (QuickMail Pro Server for MacOS 1.0.3); 14 DEC 99 11:09:25 UT >Received: (from root@localhost) > by server.ccl.net (8.8.7/8.8.7) id LAA13370 > for ccl1; Tue, 14 Dec 1999 11:37:56 -0500 >Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) > by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA12030 > for ; Tue, 14 Dec 1999 07:28:14 -0500 >Received: from chroma (chroma.yonsei.ac.kr [165.132.31.52]) > by alchemy.yonsei.ac.kr (8.8.8H2/8.8.8) with ESMTP id UAA11033 > for ; Tue, 14 Dec 1999 20:16:53 +0900 (KST) >Message-ID: <00e401bf4624$d8ed71b0$341f84a5@yonsei.ac.kr> >From: "À̼º±¤" >To: >References: <19991213104306.1428.qmail@nwcst289.netaddress.usa.net> >Subject: CCL:Electrostatic potential surface with G98/Chem3D >Date: Tue, 14 Dec 1999 20:17:38 +0900 >MIME-Version: 1.0 >Content-Type: text/plain; > charset="ks_c_5601-1987" >X-Priority: 3 >X-MSMail-Priority: Normal >X-Mailer: Microsoft Outlook Express 5.00.2919.6600 >X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 >Content-Transfer-Encoding: 8bit >X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id HAA12031 >Sender: "Computational Chemistry List" >Errors-To: chemistry-request@ccl.net >Precedence: bulk > From chemistry-request@server.ccl.net Tue Dec 14 13:24:36 1999 Received: from hotmail.com (f23.law4.hotmail.com [216.33.149.23]) by server.ccl.net (8.8.7/8.8.7) with SMTP id NAA14060 for ; Tue, 14 Dec 1999 13:24:35 -0500 Received: (qmail 16834 invoked by uid 0); 14 Dec 1999 17:11:57 -0000 Message-ID: <19991214171157.16833.qmail@hotmail.com> Received: from 196.1.114.10 by www.hotmail.com with HTTP; Tue, 14 Dec 1999 09:11:57 PST X-Originating-IP: [196.1.114.10] From: "dakshinamoorthy sivanesan" To: chemistry@ccl.net Subject: references request Date: Tue, 14 Dec 1999 09:11:57 PST Mime-Version: 1.0 Content-Type: text/plain; format=flowed hi may i ask you to give the list of references in the following topic: "photophysical properties of DNA bases". thanks in advance. regards to all CCLs. D.sivanesan research fellow chemical laboratory central leather research institute madras 600 020. INDIA ______________________________________________________ Get Your Private, Free Email at http://www.hotmail.com From chemistry-request@server.ccl.net Tue Dec 14 16:06:21 1999 Received: from marcos.networkcs.com (marcos.networkcs.com [137.66.16.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA15171 for ; Tue, 14 Dec 1999 16:06:20 -0500 Received: from us.networkcs.com (us.networkcs.com [137.66.11.15]) by marcos.networkcs.com (8.9.3/8.9.3) with ESMTP id NAA84431 for ; Tue, 14 Dec 1999 13:55:44 -0600 (CST) (envelope-from rbw@us.networkcs.com) Received: (from rbw@localhost) by us.networkcs.com (8.9.2/8.8.7) id NAA12701 for CHEMISTRY@www.ccl.net; Tue, 14 Dec 1999 13:55:44 -0600 (CST) Date: Tue, 14 Dec 1999 13:55:44 -0600 (CST) From: Richard Walsh Message-Id: <199912141955.NAA12701@us.networkcs.com> To: CHEMISTRY@server.ccl.net Subject: Gaussian98/Linda on Linux clusters ... Greetings, What has been people's experience running G98 and Linda in a Linux cluster environment? I am fairly sure that this is a supported configuration. Ease of install, nature of configuration, performance, maintenance, etc. are all of interest. A summary of replies will be posted. Thanks, and a prosperous, bug-free 2000 to all, Richard Walsh #--------------------------------------------------- # # Richard Walsh # Project Manager and Chemistry Applications Support, # Customer Support Group, # Network Computing Services, Inc. (NetworkCS) # 1200 Washington Ave. So. # Minneapolis, MN 55415 # VOX: 612-337-3467 # FAX: 612-337-3400 # EMAIL: rbw@networkcs.com # #--------------------------------------------------- # "What you can do, or dream you can, begin it; # Boldness has genius, power, and magic in it." # -Goethe #--------------------------------------------------- From chemistry-request@server.ccl.net Wed Dec 15 03:10:51 1999 Received: from jivdhan.unipune.ernet.in (jivdhan.unipune.ernet.in [196.1.114.31]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA17648 for ; Wed, 15 Dec 1999 03:10:45 -0500 Received: from chem.unipune.ernet.in (chem.unipune.ernet.in [196.1.114.10]) by jivdhan.unipune.ernet.in (8.9.0/UnipuneMailhubV1.3) with ESMTP id MAA01139 for ; Wed, 15 Dec 1999 12:22:34 +0530 Received: (from gadre@localhost) by chem.unipune.ernet.in (8.8.7/8.8.7) id MAA07726 for CHEMISTRY@www.ccl.net; Wed, 15 Dec 1999 12:22:39 +0530 Date: Wed, 15 Dec 1999 12:22:39 +0530 From: "Prof. Shridhar R. Gadre" Message-Id: <199912150652.MAA07726@chem.unipune.ernet.in> To: CHEMISTRY@server.ccl.net Subject: Summary of hydration of ions > From gammadas@netscape.net Sun Nov 28 01:23:57 1999 I would be very grateful if you would kindly forward the replies you receive and/or summarise. I have always been interested in the differences of how Phosphate and Sulfate bind to water, especiallly in view of the fact that heparin is sulfated and the phosphate analog is inactive. I think H2O---X- and other complexes have been calculated. Goutam Das ********************************************************** > From pradipta@si.fi.ameslab.gov Sat Nov 27 23:45:33 1999 Dear Prof. Gadre, One reference for hydration of F- is : J. Chem. Phys. Vol 110, No. 9, 4338, 1999. By the way, as I told you I have developed a new supermolecule-continuum solvation model. I want to send a pre-print of this paper to you. Could you kindly tell your postal address? Please give your comments after reading the paper. With best regards. Pradipta ------------------------------------------------------------------------------ > From cpye@crux.stmarys.ca Sun Nov 28 21:21:58 1999 Return-Path: Status: R You might check out some work by Sotiris Xantheas at EMSL/PNNL, Washington State, US. Also KS Sim (kim@postech.ac.kr), here are some references: J. Baik et al, JCP, 110(18), p9116-9127 (1999) - F- +Aqn n=1-6 RA Bryce et al, JPCA, 103, 4094-4100 (1999) - F- +Aq QM/MM P. Weis et al, JACS, 3531-3532 (1999) - F- + Aq C. Ebner et al,IJQC, 70, 877-886 (1998) - NO3 - + Aq OM Cabarcos et al, JCP, 110(1) p5-8 (1999) - F- + Aqn n=3-5 SS Xantheas, JPC, 100, 9703-9713 (1996) - Cl- + Aqn n=1-4 Ayotte has done a lot of experimental work on these types of systems recently. I have just published some work on lithium halide solutions in IJQC 76(1), and am preparing a paper on SO4 2- + Aq interactions, but this is probably tangential to what you are looking for. -Cory ************************************************************************** Return-Path: For what purpose? I have set up a couple of webpages for (H2O)8-10 but those results haven't been published yet. I too have a couple of different structures of (H2O)6,7. All are fully optimized and include analytical frequencies at the HF/6-31G(d,p) level of theory. If you are interested, please contact me. Regards Wolfgang Roth ===== http://www-public.rz.uni-duesseldorf.de/~rothw ===== ______________________________________________________________________ > From: Arshad Khan A number of years ago I published a paper on smaller clusters (J. Phys. Chem. vol. 99, p12450, 1995). ______________________________________________________________________ > From: Richard A Caldwell Our work is summarized in: "Calculation of the Aqueous Solvation Free Energy of the Proton," with Gregory J. Tawa, Igor Topol, R. A. Caldwell, A. Rashin, and S. K. Burt, J. Chem. Phys, 1998, 109, 4852-4863. Mostly our clusters were smaller that your targets. R. A. CAldwell ******************************************************************** ______________________________________________________________________ > From: Bernd.Hartke@RUS.Uni-Stuttgart.DE (Bernd Hartke) > You may want to check out our paper B.Hartke, M.Schuetz and H.-J.Werner, Chem.Phys. 239 (1998) 561 The corresponding ab-initio geometries (optimized at the LMP2 level with aug-cc-pVDZ basis) can be downloaded from tc1.theochem.uni-stuttgart.de by anonymous ftp: they reside in the directories "pub/severson/pentamer", "pub/severson/hexamer" and "pub/severson/heptamer", in the files "*.xyz". The corresponding energies are reported in the above paper (for the pentamer and hexamer) and in the file "pub/severson/heptamer/Comments" (for the heptamer), respectively. As far as I know, there are no ab-initio optimized geometries for n>7 (Kim et al. (Korea) is another good source, check out recent issues of JCP -- but to my knowledge he also has not tried n>7 yet). If you should find some, please tell me! You may also want to check out the paper D.J.Wales and M.P.Hodges, Chem.Phys.Lett. 286 (1998) 65 for a large-scale global optimization of water clusters up to n=21 on the TIP4P potential -- in order to convince yourself that finding a reasonable minimum structure for n=20 is a *formidable* task already on a trivial empirical potential like TIP4P. Currently, with our own newly developed global optimization strategies, we can go beyond n=21 on TIP4P, but presumably not very far... For this reason alone, I personally would not trust anybody who claims to have found the global minimum of water_n for n=10 or larger by some fully ab-initio approach. May I ask what your interest is in water clusters? Kindest regards, Bernd Hartke ______________________________________________________________________ From chemistry-request@server.ccl.net Wed Dec 15 04:07:21 1999 Received: from relay.uni-heidelberg.de (relay.uni-heidelberg.de [129.206.100.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA17953 for ; Wed, 15 Dec 1999 04:07:21 -0500 Received: from relay.urz.uni-heidelberg.de (relay-eth.urz.uni-heidelberg.de [129.206.100.201]) by relay.uni-heidelberg.de (8.9.1b+Sun/8.9.1) with ESMTP id IAA23609 for ; Wed, 15 Dec 1999 08:56:25 +0100 (MET) Received: from mail.urz.uni-heidelberg.de (mail.urz.uni-heidelberg.de [129.206.119.234]) by relay.urz.uni-heidelberg.de (8.8.8/8.8.8) with ESMTP id IAA16629 for ; Wed, 15 Dec 1999 08:55:49 +0100 (MET) Received: from aixterm9.urz.uni-heidelberg.de (ft7@aixterm9.urz.uni-heidelberg.de [129.206.119.49]) by mail.urz.uni-heidelberg.de (8.8.8/8.8.8) with ESMTP id IAA26106 for ; Wed, 15 Dec 1999 08:56:34 +0100 Received: (from ft7@localhost) by aixterm9.urz.uni-heidelberg.de (AIX4.2/UCB 8.7/8.7) id IAA25300; Wed, 15 Dec 1999 08:56:34 +0100 (CET) Date: Wed, 15 Dec 1999 08:56:34 +0100 (CET) From: Rainer Remenyi X-Sender: ft7@aixterm9.urz.uni-heidelberg.de To: chemistry@ccl.net Subject: Problems with Zindo Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id EAA17954 Dear Netters For all who have problems with Zindo in Gaussian98 this answer from gaussian.com might be interesting: ---------- Forwarded message ---------- Dr. Remenyi, Yes there does seem to be a problem and for Cu G98 is incorrectly defining the number of basis functions in the valence basis. This has been reported to the developer and should be corrected in the next minor revision. Unfortunately there is no option for doing this by manual override. Do you have source? If there is a simple fix this might be an option. Also you note that you have Rev. A.4. You should update to Rev. A.7 which we sent to all registered sites to implement some changes in defaults as well as fix a number of bugs. My correction will reference Rev. A.7 so it is worth digging this up. > Below is the result of your feedback form. It was submitted by Rainer Remenyi (ft7@ix.urz.uni-heidelberg.de) on Tuesday, December 14, 1999 at 00:33:32 > --------------------------------------------------------------------------- > > email: ft7@ix.urz.uni-heidelberg.de > > realname: Rainer Remenyi > > gver: A4 > > os: Linux, S.U.S.E > > osver: 6.2 > > subject2: Zindo Problems > > message: Hallo > > I am trying to use Zindo for calculation of UV-Vis spectra of Cu(II) Compounds. The input > > #P Zindo scf(sleazy,maxcycle=300) > > 1 2 > "Z-matrix" > > > In the Log file I get following error message: > > (Enter /var/soft/g98/l302.exe) > Do NDO one and two-electron integrals. > One-electron integrals computed using PRISM. > Generate ZINDO/S integrals. > Error: NBasis= 81 but NBZDO= 86. > Error termination via Lnk1e in /var/soft/g98/l302.exe. > > What is the reason? > > Thank you in advance > > Rainer Remenyi > Universität Heidelberg > mail ft7@ix.urz.uni-heidelberg.de > > --------------------------------------------------------------------------- > REMOTE_HOST: zr17.ub.uni-heidelberg.de > REMOTE_IDENT: > HTTP_USER_AGENT: Mozilla/4.05 [de] (WinNT; I) > From chemistry-request@server.ccl.net Wed Dec 15 11:24:09 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA20922 for ; Wed, 15 Dec 1999 11:24:09 -0500 Received: from tc.cornell.edu (LIGAND.TC.CORNELL.EDU [128.84.20.182]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id KAA16720 for ; Wed, 15 Dec 1999 10:13:19 -0500 Sender: richard@tc.cornell.edu Message-ID: <3857AC0A.FCC838BB@tc.cornell.edu> Date: Wed, 15 Dec 1999 09:56:10 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Potential from experimental density? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit It seems like it should be possible to compute an approximate "experimental" electrostatic potential of a protein given the electron density from diffraction data and assuming point charges on the nuclei. Surely this has been tried by someone? Richard Gillilan Cornell Theory Center From chemistry-request@server.ccl.net Wed Dec 15 14:13:18 1999 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22077 for ; Wed, 15 Dec 1999 14:13:18 -0500 Received: from uh.edu (Morbius.BCHS.UH.EDU [129.7.40.252]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0FMS00CTYNFN3O@Post-Office.UH.EDU> for CHEMISTRY@ccl.net; Wed, 15 Dec 1999 12:02:11 -0600 (CST) Date: Wed, 15 Dec 1999 11:59:53 -0600 From: Joe Huang Subject: A question about the RTF and Param. data in CHARMM for my ligand HPO4(2-)! To: CHEMISTRY@ccl.net, HCHuang@UH.EDU Message-id: <3857D719.FA22C978@uh.edu> Organization: BCHS, UH MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear CCLers: I am trying to do the MD simulations with CHARMM for my protein (PBP: phosphate binding protein) with ligand HPO4 (2-) positioned close to the binding pocket. I put my ligand into another segment for CHARMM to read and I am not sure if CHARMM has information for HPO4 (2-) in the RTF and Parameter files! Actually I could not find the informations for HPO4(2-) in those files! I still did the test run and view the resulting CHARMM DCD files with VMD program. In the beginning stages, the whole box with solvent, protein, xtal waters, and ligand (I have 4 segments identified as SOLV, SOLU, XWAT, and HPO4 for CHARMM) looks all right, but in the later stages, the HPO4(2-) ligand was distorted and not in the right conformation although it's moving around; some bonds in the ligand became enormously long and the angles or dihedrals were totally wrong in the ligand! Can somebody give me some ideas to solve these problems and where can I find the right parameters or rtf data for HPO4 (2-)? I will compile and organize the responses to give everybody once I solve the problems! Thanks! Merry Christmas and Happy New Year! Joe, :-) BCHS, UH HCHuang@uh.edu From chemistry-request@server.ccl.net Wed Dec 15 16:16:42 1999 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22951 for ; Wed, 15 Dec 1999 16:16:42 -0500 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id MAA26490 for chemistry@ccl.net; Wed, 15 Dec 1999 12:07:58 -0800 From: Schrodinger Info account Message-Id: <199912152007.MAA26490@canter-n-siegel.schrodinger.com> Subject: ANNC: Seminar on New Software for Drug Discovery To: chemistry@ccl.net Date: Wed, 15 Dec 1999 12:07:57 -0800 (PST) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Schrodinger is pleased to announce three upcoming seminars in California in January 2000. The seminars will examine the latest technological advances in theory and methods for modeling real world problems, including a survey of several software packages and their applications. Speakers include Professors Rich Friesner of Columbia University and Bill Goddard of Caltech. Topics include applications using Jaguar and MacroModel for catalysis, materials, biochemical and pharmaceutical research. In addition, Schrodinger's new software suite for drug discovery will be introduced. Schedule and location January 14, 2000 - Mt. View, California January 18, 2000 - San Diego, California January 21, 2000 - Pasadena, California For more information, or to register, please see http://www.schrodinger.com. If you have any questions or comments, please contact Dr. Shi-Yi Liu at Schrodinger [email: syl@schrodinger.com, phone: +1 503 299-1150]. From chemistry-request@server.ccl.net Wed Dec 15 22:06:07 1999 Received: from nuhub.dac.neu.edu (nuhub.dac.neu.edu [129.10.1.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA24341 for ; Wed, 15 Dec 1999 22:06:07 -0500 From: MARYJO@neu.edu Received: from neu.edu by neu.edu (PMDF V5.2-31 #39525) id <01JJJLOHFBXSA2DMRK@neu.edu> for CHEMISTRY@SERVER.CCL.NET; Wed, 15 Dec 1999 20:54:56 EST Date: Wed, 15 Dec 1999 20:54:55 -0500 (EST) Subject: Phosphorus basis set? To: CHEMISTRY@SERVER.CCL.NET Message-id: <01JJJLOHHH3MA2DMRK@neu.edu> X-VMS-To: CHEMISTRY@SERVER.CCL.NET MIME-version: 1.0 Hi everybody. I am trying to choose a good basis set for a phosphate P atom, and of course need the d orbitals. I am trying to find something that is compatible with GAMESS (6 components). Does anybody have any advice - opinions - suggestions? Thanks, MAry j.o.