From owner-chemistry@ccl.net Mon Nov 6 04:46:33 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA19373; Mon, 6 Nov 1995 04:39:38 -0500 Received: from fix.fsz.bme.hu for csonka@iris.inc.bme.hu by bedrock.ccl.net (8.7.1/950822.1) id EAA10183; Mon, 6 Nov 1995 04:39:00 -0500 (EST) Received: from iris.inc.bme.hu by fix.fsz.bme.hu with SMTP id AA20719 (5.65a++/IDA-BME-1.4.2 for huang@mazda.wavefun.com); Mon, 6 Nov 95 09:44:45 +0100 Received: by iris.inc.bme.hu (940816.SGI.8.6.9/920502.SGI.AUTO) id LAA20140; Mon, 6 Nov 1995 11:42:01 +0100 From: "Csonka Gabor" Message-Id: <9511061141.ZM20138@iris.inc.bme.hu> Date: Mon, 6 Nov 1995 11:41:55 +0000 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: huang@mazda.wavefun.com Subject: PM3 CRF problem Cc: chemistry@ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Wayne Huang wrote: This (the PM3 CRF problem) can be corrected by introducing a repulsive term between non-bonded hydrogens into the PM3 energy expression, which allows it rapidly approaches to zero with increasing H--H distance and becomes insignificant for distances greater than about 2 angstrom. Comments: This may solve the H-H problem, but i will not solve e.g. the O-H problem. One should introduce a different H CRF, which work correctly. Gabor -- Gabor I. Csonka Budapest University of Technology FAX: (361) 463.36.42 Inorganic Chemistry Dept. Ch. Bldg csonka@iris.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 http://www.fsz.bme.hu/bme/chemical/csonka.html From arne@rune.biokemi.su.se Mon Nov 6 06:01:35 1995 Received: from rune.biokemi.su.se. for arne@rune.biokemi.su.se by www.ccl.net (8.6.10/950822.1) id FAA19732; Mon, 6 Nov 1995 05:47:50 -0500 Received: by rune.biokemi.su.se. (5.x/SMI-SVR4) id AA11032; Mon, 6 Nov 1995 11:47:19 GMT Date: Mon, 6 Nov 1995 11:47:19 GMT From: arne@rune.biokemi.su.se (Arne Elofsson) Message-Id: <9511061147.AA11032@rune.biokemi.su.se.> To: CHEMISTRY@ccl.net Cc: chemistry@www.ccl.net In-Reply-To: Richard Macdonald's message of Thu, 2 Nov 1995 13:33:12 -0800 Subject: Re: CCL:Asilomar conf paper References: <01BAA927.C279F0A0@intel5.biosym.com> In article <01BAA927.C279F0A0@intel5.biosym.com> Richard Macdonald writes: > > I remember reading a write-up of the protein modeling challenge > held at Asimomar recently (I think it was in Protein Science). > But I can not find it now. > > Could some kind soul point me to the reference? > If I remember correctly they will appear in proteins and very soon, but I haven't seen them yet arne (To think before you speak is as to wipe your ass before you shit.) ----------------------------------------------------------------- From: Arne Elofsson Email: arne@biokemi.su.se WWW: http://www.doe-mbi.ucla.edu/people/arne/main.html From owner-chemistry@ccl.net Mon Nov 6 06:16:34 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id FAA19730; Mon, 6 Nov 1995 05:47:50 -0500 Received: from rune.biokemi.su.se. for arne@rune.biokemi.su.se by bedrock.ccl.net (8.7.1/950822.1) id FAA10305; Mon, 6 Nov 1995 05:47:46 -0500 (EST) Received: by rune.biokemi.su.se. (5.x/SMI-SVR4) id AA11032; Mon, 6 Nov 1995 11:47:19 GMT Date: Mon, 6 Nov 1995 11:47:19 GMT From: arne@rune.biokemi.su.se (Arne Elofsson) Message-Id: <9511061147.AA11032@rune.biokemi.su.se.> To: CHEMISTRY@ccl.net Cc: chemistry@www.ccl.net In-Reply-To: Richard Macdonald's message of Thu, 2 Nov 1995 13:33:12 -0800 Subject: Re: CCL:Asilomar conf paper References: <01BAA927.C279F0A0@intel5.biosym.com> In article <01BAA927.C279F0A0@intel5.biosym.com> Richard Macdonald writes: > > I remember reading a write-up of the protein modeling challenge > held at Asimomar recently (I think it was in Protein Science). > But I can not find it now. > > Could some kind soul point me to the reference? > If I remember correctly they will appear in proteins and very soon, but I haven't seen them yet arne (To think before you speak is as to wipe your ass before you shit.) ----------------------------------------------------------------- From: Arne Elofsson Email: arne@biokemi.su.se WWW: http://www.doe-mbi.ucla.edu/people/arne/main.html From owner-chemistry@ccl.net Mon Nov 6 06:30:00 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id GAA19848; Mon, 6 Nov 1995 06:13:29 -0500 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by bedrock.ccl.net (8.7.1/950822.1) id GAA10420; Mon, 6 Nov 1995 06:13:26 -0500 (EST) Date: Mon, 6 Nov 95 6:10:45 EST From: George R Famini To: chemistry@ccl.net Subject: New Orleans ACS Meeting Organization: Division of Computers in Chemistry Priority: Normal Message-ID: <9511060610.aa10525@cbdcom.apgea.army.mil> This is a reminder for all of you who plan to attend and present a paper at the New Orleans American Chemical Society meeting March 24-28, 1996. The deadlines for abstract submission vary between the different divisions. The deadline for the Division of Computers in Chemistry WAS October 20. Other divisions are much later, just before Thanksgiving. If anyone is still planning to submit an abstract to COMP for this meeting, I suggest you contact me immediately. General poster and oral abstracts can be sent to me by priority or overnight mail. For presentations in one of the symposia, I suggest you contact the either organizer or me immediately. George Famini COMP Program Chair From varnali@ds5500.cc.boun.edu.tr Mon Nov 6 08:46:37 1995 Received: from ds5500.cc.boun.edu.tr for varnali@ds5500.cc.boun.edu.tr by www.ccl.net (8.6.10/950822.1) id IAA20997; Mon, 6 Nov 1995 08:43:40 -0500 Received: by ds5500.cc.boun.edu.tr; (5.65/1.1.8.2/26Dec94-8.2MPM) id AA04443; Mon, 6 Nov 1995 15:10:51 -0500 Date: Mon, 6 Nov 1995 15:10:51 -0500 (EST) From: "YARD.DOC. TEREZA VARNALI" X-Sender: varnali@ds5500.cc.boun.edu.tr To: chemistry@www.ccl.net Subject: semiempirical calculations on a complex of Co and Sn. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am interested to run semiempirical calculations on a Cobalt complex that undergoes a reaction with HSnPh3. The transition state and the product therefore incorporates both Co and Sn atoms . The problem is that I am unaware of a program that is parametrized for both Co and Sn. PM3 is parametrized for Sn and ZINDO1 is parametrized for Co ... My computational facilities are limited but if you can suggest basis set that will not be costly I can try that too. I wellcome all suggestions on the subject. Thanks Tereza Varnali Varnali@ds5500.cc.boun.edu.tr From yu@infinity.wavefun.com Mon Nov 6 11:01:37 1995 Received: from volvo.wavefun.com for yu@infinity.wavefun.com by www.ccl.net (8.6.10/950822.1) id KAA24770; Mon, 6 Nov 1995 10:46:06 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA11682; Mon, 6 Nov 95 07:45:10 -0800 Received: from infinity.wavefun.com(198.147.95.8) by volvo.wavefun.com via smap (V1.3) id sma011680; Mon Nov 6 07:44:46 1995 Received: by infinity.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:sopekmir@mitr.p.lodz.pl id AA03662; Mon, 6 Nov 95 07:44:06 -0800 From: "yu" Message-Id: <9511060744.ZM3660@infinity.wavefun.com> Date: Mon, 6 Nov 1995 07:44:06 -0800 Reply-To: yu@volvo.wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: CHEMISTRY@www.ccl.net Subject: Li and Ca in PM3 Cc: sopekmir@mitr.p.lodz.pl Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Nov 4, 2:42pm, Miroslaw Sopek wrote: > Subject: CCL:Na,Li,Ca in Pm3 and Am1 > Hello netters, > Is anybody on the net aware of any trial > of adding parameters for 'Na' and 'Li' to PM3 > and 'Na' for AM1 ('Li' is already present). > The same question about parameters for 'Ca' > in both methods. > > I will summarize the answers for the net, > Mirek > > ---------------------------------------------- > dr Miroslaw Sopek > Institute of Applied Radiation Chemistry > Lodz, Poland > ----------------------- sopekmir@mitr.p.lodz.pl > Anders et.al have published their Li parameters on PM3 (J. Copmt. Chem., 14(11), 1301(1993). In Wavefunction, Inc, I have almoust finished the parameterization of Ca and will release it soon. Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92715 | \/ | Lao-tzu (604-531 B.C.)| +-----------------------+------------------+-------------------------+ From owner-chemistry@ccl.net Mon Nov 6 11:16:37 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA24984; Mon, 6 Nov 1995 11:02:23 -0500 Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA12762; Mon, 6 Nov 1995 11:02:21 -0500 (EST) From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #10002) id <01HXBJUNRCL8A23AQ7@vms.cis.pitt.edu>; Mon, 06 Nov 1995 11:02:10 -0400 (EDT) Date: Mon, 06 Nov 1995 11:02:10 -0400 (EDT) Subject: Computational Chemistry Persons Role/Duties in Chemistry Dept. To: chemistry@ccl.net Message-id: <01HXBJUNRCLAA23AQ7@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, I would appreciate if some of you who are holding positions as Computational Chemistry (Hardware/ Software / Teaching) related posposoi From owner-chemistry@ccl.net Mon Nov 6 11:31:38 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA25207; Mon, 6 Nov 1995 11:17:41 -0500 Received: from myriad.cis.pitt.edu for SATYAM@vms.cis.pitt.edu by bedrock.ccl.net (8.7.1/950822.1) id LAA12898; Mon, 6 Nov 1995 11:17:39 -0500 (EST) From: Received: from vms.cis.pitt.edu by vms.cis.pitt.edu (PMDF V4.3-10 #10002) id <01HXBK80UK00A23AQ7@vms.cis.pitt.edu>; Mon, 06 Nov 1995 11:17:32 -0400 (EDT) Date: Mon, 06 Nov 1995 11:17:32 -0400 (EDT) Subject: Compuational Chemist's Role in Chemistry Department- To: chemistry@ccl.net Message-id: <01HXBK80VMKYA23AQ7@vms.cis.pitt.edu> X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear Netters, Sorry for the earlier truncated message.. I lost connection to my account on VMS The full question follows :: I would appreciate very much if people who have Computational Chemistry position in CHEMISTRY DEPARTMENT (either for teaching/ Hardware/Software) would contact me and let me know the role they play in upkeep of the computational facilities and labs or direct me to their home pages. Thanks a lot. Regards Satyam From owner-chemistry@ccl.net Mon Nov 6 11:46:39 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id LAA25380; Mon, 6 Nov 1995 11:27:26 -0500 Received: from volta for aiba@ir.phys.chem.ethz.ch by bedrock.ccl.net (8.7.1/950822.1) id LAA13054; Mon, 6 Nov 1995 11:27:16 -0500 (EST) Date: Mon, 6 Nov 1995 17:27:08 +0100 Message-Id: <95110617270795@ir.phys.chem.ethz.ch> From: aiba@ir.phys.chem.ethz.ch (Ayaz Bakasov, Phys. Chem., ETH Zurich) To: chemistry@ccl.net Subject: G: to G92 gurus X-VMS-To: smtp%"chemistry@ccl.net" X-VMS-Cc: AIBA Dear Gurus of G92/94, Something for you here please. I have run two a bit different G92 jobs and got astoundingly different results. I.e. one job failed in Lnk1e, while the second successfully completed. Why?! An explanation will be so much appreciated. If any of you think they can figure it out, waisting not so much of your valuable time, I would be glad to supply more of the output from these puzzling jobs. Remark: I am putting beneath the error piece of the output of the failed job and both inputs, failed and successful. The platform is DEC AXP. But the same is on IBM RS6000/590 with AIX, with that difference in error message that UNIX systems complains about "memory fault". I honestly tried to "format" a bit these pieces of I/O, though one knows that not so much could be done about it. Best regards, Ayaz Bakasov. ******************************************** Now, to details. The molecule is the same for both jobs: N2O4. The method is the same: CIS. The ONLY difference is in geometry: -- the first job is for planar geometry (D2H); -- the second one - for twisted geometry (D2). Both jobs completed RHF stage with the standard message "SCF DONE". The failure apparently occurs at the beginning of the CIS stage for the "planar" job. [I wonder why. The symmetry is higher so it must in principle require less memory for storage or whatever manipulation is sought in Davidson procedure.] So, the first job failed some time after "SCF DONE", with the following message: > RHF GROUND STATE > Number of initial states reduced to 1000 > due to Davidson diagonalization limit of 2000. > MDV IS: 7000000 > Making orbital integer symmetry assigments: > ORBITAL SYMMETRIES. > OCCUPIED (B3G) (B2U) (B1U) (AG) (AG) (B1U) (AG) (B1U) (B2U) > (B3G) (AG) (B1U) (AG) (B3U) (B2G) (B2U) (B1U) > (B3G) (AG) (B1G) (AU) (B2U) (B3G) > VIRTUAL (B1U) (B3U) (B2G) (B2U) (B3G) (AG) (B1U) (B3U) > (B2U) (AG) (B1U) (B2G) (AG) (B3G) (B2U) (B3U) > (B1U) (B3G) (B1G) (AU) (AG) (B2G) (B1U) (AG) (B3G) > (B2U) (B1U) (AG) (B1U) (B2U) (B3G) > 527 initial guesses have been made. > Convergence on wavefunction: 0.000100000000000 > Davidson Disk Diagonalization is being used. > MSek= 527 requested MaxMI= 200 MaxDav= 2000. > Error termination in Lnk1e. ******************* ******************* INPUTS: ******* The two inputs are these (they differ ONLY in dihedral angle, for the 1st job it is zero, for the second one it is 60.0): %%%%%%%%%% "PLANAR" INPUT (which failed) %%%%%%%% %Mem=7000000 Default route: MAXDISK=30000000 ----------------------------------------------------- #CIS(NSTATES=200,TRIPLETS) 6-31G SCF=DIRECT IOp(9/40=3) FChk=MO ------------------------------------------------------ 1/29=10000/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,11=9,25=1,30=1/1,2,8,3; 4//1; 5/5=2,38=4/2; 8/6=1,10=1,27=30000000/1,4; 9/27=30000000,40=3,41=200,42=3,48=3/14; 6/7=2,8=2,9=2,10=2,19=1/1; 99/5=1,9=1/99; --------------------- 631G; N2O4 PLANAR !!! --------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 N N 1 1.786 O 1 1.208 2 135.3 O 1 1.208 2 135.3 3 180. 0 O 2 1.208 1 135.3 3 0. 0 O 2 1.208 1 135.3 3 180. 0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%% "TWISTED" INPUT (successful!) %%%%%%%%%%% %Mem=7000000 Default route: MAXDISK=30000000 ------------------------------------------------------ #CIS(NSTATES=200,TRIPLETS) 6-31G SCF=DIRECT IOp(9/40=3) FChk=MO --------------------------------------------------- 1/29=10000/1; 2/12=2,17=6,18=5/2; 3/5=1,6=6,11=9,25=1,30=1/1,2,8,3; 4//1; 5/5=2,38=4/2; 8/6=1,10=1,27=30000000/1,4; 9/27=30000000,40=3,41=200,42=3,48=3/14; 6/7=2,8=2,9=2,10=2,19=1/1; 99/5=1,9=1/99; ------------------------------ 631G; N2O4 TWISTED TO 60 DEGREES. ------------------------------ Symbolic Z-matrix: Charge = 0 Multiplicity = 1 N N 1 1.786 O 1 1.208 2 135.3 O 1 1.208 2 135.3 3 180. 0 O 2 1.208 1 135.3 3 60. 0 O 2 1.208 1 135.3 3 240. 0 From gmercier@helix.nih.gov Mon Nov 6 12:16:40 1995 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.6.10/950822.1) id MAA26301; Mon, 6 Nov 1995 12:05:05 -0500 Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.12/8.6.12) with SMTP id MAA10448 for ; Mon, 6 Nov 1995 12:05:02 -0500 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 6 Nov 1995 13:14:57 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: starburst dendrimers coordinates Hi! Before I rediscover the wheel I would like to know if anyone is aware of a program to generate coordinates for a starburst dendrimer given its core and unit fragments. Alternatively, is there a repository of some of these coordinates, similar to those for C60? Thanks? Gustavo A. Mercier, Jr. M.D.-Ph.D. NIH - LDRR OD OIR LDRR Building 10 Room B1N256 10 Center Dr MSC 1074 Bethesda, Maryland 20892-1074 phone: 301-402-3586, 301-496-1981 fax: 301-402-3216 e-mail: gmercier@helix.nih.gov From owner-chemistry@ccl.net Mon Nov 6 13:01:40 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id MAA27232; Mon, 6 Nov 1995 12:50:04 -0500 Received: from gtc05f for vis@gensia.com by bedrock.ccl.net (8.7.1/950822.1) id MAA13977; Mon, 6 Nov 1995 12:50:01 -0500 (EST) Received: from genny (genny.res.gensia.com) by gtc05f (5.x/SMI-SVR4) id AA21315; Mon, 6 Nov 1995 09:44:50 -0800 Received: by genny (940816.SGI.8.6.9/930416.SGI.AUTO) id MAA26860; Mon, 6 Nov 1995 12:49:16 GMT Date: Mon, 6 Nov 1995 04:49:15 +48000 From: Viswanadhan To: chemistry@ccl.net Subject: Re: Parametrization for Zinc / charges & vdW radius Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Netters, We have been trying to develop parameters for the Zinc ion in the active site of an enzyme ( a fairly typical problem). The ion is surrounded by three neutral histidines, a charged carboxylate and a hydroxyl group of an inhibitor/ligand. We performed MOPAC6.0 (with AM1 & MNDO Hamiltonians) on a model system (single point calculation) and we obtain a value of approx. +0.7 on Zinc (Mulliken charge). Gaussian 94 calculations at 3-21G* level indicate a higher Mulliken charge of approx. 1.0. I would like to use CHELPG charges which necessitates the use of right vdW radii. For neutral Zinc, the Bondi radius (J. Phys. Chem. 68. 441) is 1.39 A, which is clearly not appropriate. Can any one point to recent references or suggest a method? I will be happy to summarize the responses (with regard to vdW radii & modeling the charge in the active site of an enzyme for the Zinc ion). Vellarkad N. Viswanadhan vis@gensia.com From yu@infinity.wavefun.com Mon Nov 6 13:04:09 1995 Received: from volvo.wavefun.com for yu@infinity.wavefun.com by www.ccl.net (8.6.10/950822.1) id MAA27135; Mon, 6 Nov 1995 12:46:01 -0500 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA11892; Mon, 6 Nov 95 09:40:08 -0800 Received: from infinity.wavefun.com(198.147.95.8) by volvo.wavefun.com via smap (V1.3) id sma011888; Mon Nov 6 09:40:06 1995 Received: by infinity.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:varnali@boun.edu.tr id AA03897; Mon, 6 Nov 95 09:39:27 -0800 From: "yu" Message-Id: <9511060939.ZM3895@infinity.wavefun.com> Date: Mon, 6 Nov 1995 09:39:26 -0800 Reply-To: yu@volvo.wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: chemistry@www.ccl.net Subject: Co parameters in PM3 Cc: varnali@boun.edu.tr Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hi Netters, On Nov 6, 3:10pm, YARD.DOC. TEREZA VARNALI wrote: > Subject: CCL:semiempirical calculations on a complex of Co and Sn. > Hi, > I am interested to run semiempirical calculations on a Cobalt complex > that undergoes a reaction with HSnPh3. The transition state and the > product therefore incorporates both Co and Sn atoms . The problem is that > I am unaware of a program that is parametrized for both Co and Sn. > PM3 is parametrized for Sn and ZINDO1 is parametrized for Co ... > My computational facilities are limited but if you can suggest basis set > that will not be costly I can try that too. > I wellcome all suggestions on the subject. > Thanks > Tereza Varnali > Varnali@ds5500.cc.boun.edu.tr > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: varnali@ds5500.cc.boun.edu.tr > -- Original Sender From: Address: varnali@boun.edu.tr > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > >-- End of excerpt from YARD.DOC. TEREZA VARNALI I have developed the Co parameters in PM3 ( and othet metels, such as Cu, Ni, Fe, Mn, Cr, Ti, ..., too) and we call our method PM3(TM). Our package, SPARTAN, can do PM3(TM) calculations. If you interested, please contact sales@wavefun.com Thanks, Jianguo Yu -- +-----------------------+------------------+-------------------------+ |Jianguo Yu, Ph.D. | ______________ | E-Mail: yu@wavefun.com | |Computational Chemist | \ _________ / | Phone: (714)955-2120 | |Wavefunction Inc. | \ \\\\\\\\/ | Fax: (714)955-2118 | |18401 Von Karman | \ \\\\\/ | "The doctrines observe | |Suite 370 | \ \\/ | nature" | |Irvine, CA 92715 | \/ | Lao-tzu (604-531 B.C.)| +-----------------------+------------------+-------------------------+ From owner-chemistry@ccl.net Mon Nov 6 13:31:42 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA27766; Mon, 6 Nov 1995 13:21:08 -0500 Received: from volvo.wavefun.com for huang@mazda.wavefun.com by bedrock.ccl.net (8.7.1/950822.1) id NAA14269; Mon, 6 Nov 1995 13:19:44 -0500 (EST) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA11933; Mon, 6 Nov 95 10:17:32 -0800 Received: from mazda.wavefun.com(198.147.95.6) by volvo.wavefun.com via smap (V1.3) id sma011931; Mon Nov 6 10:17:15 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA05743; Mon, 6 Nov 95 10:16:35 -0800 From: "Wayne Huang" Message-Id: <9511061016.ZM5741@mazda.wavefun.com> Date: Mon, 6 Nov 1995 10:16:35 -0800 In-Reply-To: "YARD.DOC. TEREZA VARNALI" "CCL:semiempirical calculations on a complex of Co and Sn." (Nov 6, 3:10pm) References: Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: "YARD.DOC. TEREZA VARNALI" Subject: Re: CCL:semiempirical calculations on a complex of Co and Sn. Cc: chemistry@ccl.net Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Regarding the quest for a program have both Co and Sn paramters: Spartan semiempirical PM3(tm) module has Co parameters, along with original Sn PM3 parameters, which should be able to deal with your system. This module has been actively under development the past year or so, along with our DFT module, aiming to provide tools for transition metals modeling. Currently PM3(TM), which includes d-orbitals, has parameters for total of 14 d transition metals (Ti, Cr, Mn, Fe, Co, Ni, Cu, Zr, Mo, Rh, Pd, Hf, Ta and W) plus Gd from La series. In additional of TM parameters. Boron parameters are also available for PM3 method. The intial results these parameters seem to be promising. I could send you some of these calculations if you want or run some calculations on your test molecules. Please feel free to contact me if you have any question. --Wayne -- +---------------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92715 | | Wavefunction, Inc. | (714)955-2120 Fax: (714)955-2118 | | huang@wavefun.com | World Wide Web: http://wavefun.com | +---------------------------------------------------------------------+ From cramer@maroon.tc.umn.edu Mon Nov 6 17:16:44 1995 Received: from maroon.tc.umn.edu for cramer@maroon.tc.umn.edu by www.ccl.net (8.6.10/950822.1) id RAA02652; Mon, 6 Nov 1995 17:12:44 -0500 Received: by maroon.tc.umn.edu; Mon, 6 Nov 95 15:53:23 -0600 Message-Id: <309e83d3301b002@maroon.tc.umn.edu> From: Christopher J Cramer Subject: COMP WWW page To: chemistry@www.ccl.net Date: Mon, 6 Nov 1995 15:53:22 -0600 (CST) Cc: kate_holloway@merck.com (Kate Holloway), grfamini@cbda9.apgea.army.mil (George R Famini), theochem@ctc.com X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 569 Just to alert CCL readers that the Computers in Chemistry Division of the American Chemical Society has opened a Web site. It is newborn, so comments are welcome on various aspects (see the page). Site is http://hackberry.chem.niu.edu/COMP/ Thanks to Steven Bachrach at NIU for considerable support. CJC -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-7541 cramer@maroon.tc.umn.edu http://dionysus.chem.umn.edu/ From echamot@xnet.com Mon Nov 6 19:16:45 1995 Received: from flood.xnet.com for echamot@xnet.com by www.ccl.net (8.6.10/950822.1) id TAA04556; Mon, 6 Nov 1995 19:05:36 -0500 Received: from echamot.xnet.com by flood.xnet.com (8.7/XNet-1.4R) with SMTP id RAA00437; Mon, 6 Nov 1995 17:56:35 -0600 (CST) Message-ID: Date: Mon, 6 Nov 95 18:02:03 CST From: "Ernest Chamot" Subject: Re: CCL:starburst dendrimers coordinates To: "Gustavo A. Mercier, Jr." , chemistry@www.ccl.net X-Mailer: VersaTerm Link v1.1.6 Hi Gustavo, Your in luck! >Before I rediscover the wheel I would like to know if anyone is aware of >a program to generate coordinates for a starburst dendrimer given >its core and unit fragments. Alternatively, is there a repository of >some of these coordinates, similar to those for C60? I don't know about a repository of coordinates, but there was a poster given just last week at the Midland Section ACS meeting on exactly that: software they have developed and are using to build dendrimers for modeling. I believe they are up to 7th generation dendrimers and higher, depending on whether you use a divergent synthesis or a convergent synthesis. The email address I have for Leela Rakesh, at Central Michigan University, is: 37WLWOO@CMUVM EC --- Ernest Chamot Consultant in Computational Chemistry Applications Chamot Laboratories, Inc. 530 E. Hillside Rd. Naperville, Illinois 60540 echamot@xnet.com From xiaopeng@astro.ocis.temple.edu Mon Nov 6 19:46:45 1995 Received: from astro.ocis.temple.edu for xiaopeng@astro.ocis.temple.edu by www.ccl.net (8.6.10/950822.1) id TAA04899; Mon, 6 Nov 1995 19:38:07 -0500 Received: (from xiaopeng@localhost) by astro.ocis.temple.edu (8.7.1/8.7.1) id RAA15997; Mon, 6 Nov 1995 17:27:22 -0500 (EST) Date: Mon, 6 Nov 1995 17:27:20 -0500 (EST) From: Peking To: chemistry@www.ccl.net Subject: relaxed potential surface scan with Gaussian 94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, CCls, When I run the relaxed potential surface scan using Gaussian 94. The computer give me "Input z-matrix variables are not compatible with final structure." and "ERRor termination" Anybody can give me some idea what I did wrong here and how to avoid? Many thanks! xiaopeng ======================================================= Chemistry Graduate student 215-2047149(office) xiaopeng@astro.ocis.temple.edu ====================================================== From owner-chemistry@ccl.net Mon Nov 6 20:46:46 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id UAA05496; Mon, 6 Nov 1995 20:35:33 -0500 Received: from cheetah.it.wsu.edu for brian@bert.chem.wsu.edu by bedrock.ccl.net (8.7.1/950822.1) id UAA18713; Mon, 6 Nov 1995 20:35:30 -0500 (EST) Received: from bert.chem.wsu.edu (bert.chem.wsu.edu [134.121.43.22]) by cheetah.it.wsu.edu (8.6.12/WSUit-1.1) with SMTP id RAA10418 for ; Mon, 6 Nov 1995 17:35:32 -0800 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA19107; Mon, 6 Nov 1995 17:35:57 -0800 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9511070135.AA19107@bert.chem.wsu.edu> Subject: Re: CCL:G:Parametrization for Zinc / charges & vdW radius To: vis@gensia.com (Viswanadhan) Date: Mon, 6 Nov 1995 15:57:04 -0800 (PST) In-Reply-To: from "Viswanadhan" at Nov 6, 95 04:49:15 am X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Sender: brian@bert.chem.wsu.edu Viswanadhan wrote: : : : I would like to use CHELPG charges which necessitates the use of right : vdW radii. For neutral Zinc, the Bondi radius (J. Phys. Chem. 68. 441) : is 1.39 A, which is clearly not appropriate. Can any one point to recent : references or suggest a method? I will be happy to summarize the : responses (with regard to vdW radii & modeling the charge in the active : site of an enzyme for the Zinc ion). : : Vellarkad N. Viswanadhan : Yes, what does constitute "good" vdW radii. In our work on Fe-S centers in proteins we've noticed that the actual charges calculated by CHELPG vary significantly depending on whether you use Breneman&Wiberg radii or Gavizotti&Spackman radii. Generally, Breneman & Wiberg based charges seem "better behaved" in our systems. Also, we've noticed that many groups use radii designed for other purposes and "plug" these into the CHELPG algorithm. What are the rationals people use in choosing their radii? -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| brian@bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | brian_beck@wsu.edu | |\ - *|| WSU , 206 Fulmer | URL http://elmo.chem.wsu.edu/~brian | | | || Pullman, WA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From chatt@tniri.go.jp Mon Nov 6 22:01:47 1995 Received: from ripspost.aist.go.jp for chatt@tniri.go.jp by www.ccl.net (8.6.10/950822.1) id VAA06146; Mon, 6 Nov 1995 21:53:29 -0500 Received: from tnhost.tniri.go.jp by ripspost.aist.go.jp (8.6.9+2.4W/TISN-1.3/R2-AIST) id LAA29712; Tue, 7 Nov 1995 11:53:22 +0900 Received: by tnhost.tniri.go.jp (4.1/6.4J.6-tniri.MASTER) id AA23888; Tue, 7 Nov 95 11:52:54 JST Date: Tue, 7 Nov 95 11:52:54 JST From: chatt@tniri.go.jp (Abhijit Chatterjee) Message-Id: <9511070252.AA23888@tnhost.tniri.go.jp> To: CHEMISTRY@www.ccl.net Subject: MEMBERSHIP Dear Sir, I want to access CCL, please make me a member. With best regards Abhijit Chattopadhyay email : chatt@tniri.go.jp