From chemistry-request@server.ccl.net Wed Apr 3 02:22:38 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g337Mcp05480 for ; Wed, 3 Apr 2002 02:22:38 -0500 Received: from eden.rutgers.edu (er2.rutgers.edu [165.230.180.148]) by goshen.rutgers.edu (Postfix) with ESMTP id 250481FD26 for ; Wed, 3 Apr 2002 02:22:33 -0500 (EST) Received: by eden.rutgers.edu (Postfix, from userid 37805) id 6FEB6AFDC; Wed, 3 Apr 2002 02:22:29 -0500 (EST) Date: Wed, 3 Apr 2002 02:22:29 -0500 (EST) From: Jianquan Chen X-Sender: jianquan@er2.rutgers.edu To: chemistry@ccl.net Subject: How to compile the latest Rasmol using Visual C++ 6 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, Can any one tell me how to compile the RasMol_2.7.1.1 using Visual C++? ANd where can I get the source codes of Rasmol2.7.2.1? Thank you. Jianquan Chen From chemistry-request@server.ccl.net Wed Apr 3 06:02:21 2002 Received: from web12806.mail.yahoo.com ([216.136.174.41]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g33B2Lp11461 for ; Wed, 3 Apr 2002 06:02:21 -0500 Message-ID: <20020403110211.67078.qmail@web12806.mail.yahoo.com> Received: from [203.87.132.164] by web12806.mail.yahoo.com via HTTP; Wed, 03 Apr 2002 03:02:11 PST Date: Wed, 3 Apr 2002 03:02:11 -0800 (PST) From: amor san juan Subject: Non-integral charge problem:AutoDockTools To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Fellow dockers: Nice day to all! Would someone please help me in preparing macromolecules for docking. Under AutoDockTools, I encountered hanging of the program after reading the pdb macromolecule file. The warning displays "non-integral charge". Any ideas will be appreciated. Amor San Juan University of the Philippines __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Tue Apr 2 19:33:43 2002 Received: from post.webmailer.de ([192.67.198.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g330Xhp26591 for ; Tue, 2 Apr 2002 19:33:43 -0500 Received: from baaden.biop.ox.ac.uk (baaden.biop.ox.ac.uk [163.1.16.24]) by post.webmailer.de (8.9.3/8.8.7) with ESMTP id CAA22859; Wed, 3 Apr 2002 02:33:37 +0200 (MET DST) Message-Id: <200204030033.CAA22859@post.webmailer.de> To: chemistry@ccl.net, Jelena Tamuliene Subject: Re: CCL:magnetic shielding tensors In-reply-to: Your message of "Wed, 27 Mar 2002 13:03:20 +0200." X-image-url: http://crypt.u-strasbg.fr/marc/m-baaden.gif X-url: X-face: -Nz&SN]%I8g9WFR#/!fe9se!_G_OndNloj@t+6jrGsoZ"z)?an0n P!Nls~*o?u7fy:]1N|^^(KX*uE>Nk{bHaCJ)(hXF~E#5)j.k0n4hgfIzpmn,[VY'\7X:;VOZ\CItIq G!2f8,k2`VLrkXQ:<.3LxEQ'E-;d:A)V# Date: Wed, 03 Apr 2002 01:33:26 +0100 From: Marc Baaden Dear all, sorry for the late answer, I meant to reply earlier, but the Easter break got in between ... Concerning Jelena's question about magnetic shielding tensors as calulated by Gaussian, I can give the following hints from previous work we did. A short discussion of the tensor can also be found in our paper in Mol. Phys. 2000, 98, 329-342 and more importantly the relevant references cited therein (concerning the tensor I would also strongly recommend the book by Hans W. Spiess, but I don't have the reference at hand). It is indeed the asymmetric tensor which is calculated by Gaussian, and it has to be decomposed to obtain the standard parameters usually used. The isotropic shielding is defined as sigma_iso = 1/3 * trace(Tensor) The symmetrical part of the tensor is obtained by Tens_sym = 1/2 * (Tensor_ij + Tensor_ji) For the principal axes and values, the symmetric tensor Tens_sym has to be diagonalized and its eigenvalues are the principal values called sigma_11, sigma_22 and sigma_33. The eigenvectors are the principal axes. One convention for the naming of the axes (11, 22, 33) is that sigma_11 <= sigma_22 <= sigma_33 Then anisotropy delta_sigma and asymmetry eta depend on sigma_11, sigma_33 and sigma_iso: If | sigma_11 - sigma_iso| >= |sigma_33 - sigma_iso | then delta_sigma = 3/2 * (sigma_iso - sigma_11) sigma_22 - sigma_33 eta = -------------------- sigma_11 - sigma_iso If | sigma_11 - sigma_iso| < |sigma_33 - sigma_iso | then delta_sigma = 3/2 * (sigma_iso - sigma_33) sigma_22 - sigma_11 eta = -------------------- sigma_33 - sigma_iso Note: The above definition of the anisotropy is NOT the same as the one used/calculated by Gaussian, as they follow another convention. NB: No warranties concerning typos .. All the best, Marc Baaden From chemistry-request@server.ccl.net Wed Apr 3 05:06:06 2002 Received: from uni-kl.de ([131.246.137.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33A65p10001 for ; Wed, 3 Apr 2002 05:06:05 -0500 Received: from aixs1.rhrk.uni-kl.de (aixs1.rhrk.uni-kl.de [131.246.137.3]) by uni-kl.de (8.11.6+Sun/8.11.5) with ESMTP id g33A5wr28364 for ; Wed, 3 Apr 2002 12:05:58 +0200 (MET DST) Received: from aixd1.rhrk.uni-kl.de ([131.246.137.210] ident=exim) by aixs1.rhrk.uni-kl.de with esmtp (Exim 3.33 #2) id 16sheQ-0006Q2-00 for CHEMISTRY@server.ccl.net; Wed, 03 Apr 2002 12:05:58 +0200 Received: from gerwalin (helo=localhost) by aixd1.rhrk.uni-kl.de with local-esmtp (Exim 3.03 #5) id 16sheQ-000R0C-00 for CHEMISTRY@server.ccl.net; Wed, 03 Apr 2002 12:05:58 +0200 Date: Wed, 3 Apr 2002 12:05:57 +0200 (MES) From: Elmar Gerwalin To: CHEMISTRY@server.ccl.net Subject: Semiempirical calc. of K with g98 ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I'd like to do semiempirical calculations containing K (potassium) and would like to know which method (that's implemented in g98!) is best or if it's possible to generate or add parameters for K to g98. ( I found from http://www.chamotlabs.com/Freebies/Table/parameters-table.html that INDO/1 parameters exist, but this is not available in g98 ) Thanks for any help in advance! Bye Elmar ============================================================== Elmar Gerwalin , University of Kaiserslautern, Germany gerwalin@rhrk.uni-kl.de (soon: ) http://www.rhrk.uni-kl.de/~gerwalin ============================================================== From chemistry-request@server.ccl.net Wed Apr 3 10:20:11 2002 Received: from nikias.cc.uoa.gr ([195.134.68.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33FKAp18285 for ; Wed, 3 Apr 2002 10:20:10 -0500 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id SAA05318 for ; Wed, 3 Apr 2002 18:20:00 +0300 (EET DST) Date: Wed, 3 Apr 2002 18:20:00 +0300 (EET DST) From: Ioannis Kerkines To: chemistry@ccl.net Subject: G98 CASSCF Efficiency Considerations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear listmembers, I am trying to perform with Gaussian 98 a CASSCF calulation with 4 electrons in 4 orbitals for a diatomic molecule using a basis set of 224 functions. I have encountered many problems so far regarding efficiency and I would like to ask if anybody has any experience with this. First of all, I am unable to do a "conventional" (SCF=Conven) calculation because I have g functions in the basis set, whereas the subroutine performing "conventional" calculations suppotrs only up to f functions. The direct calculation of integrals needs much memory which is not available. In fact I get a message: InCore calculation needs more space: 341070520 In this calculation the integrals will be calculated in every iteration and Contracted with The Density Matrices so the actual ("direct") calculation needs very much time to be done. Furthermore, the CASSCF iterations after approaching convergence (very very slowly), they start to diverge (very very slowly again), until reaching the max. no of iterations (64 in this case) and then stop. I tried to change the convergence options by imposing quadratic convergence ( (CASSCF,4,4,QC,FullDiag) but no luck, I get an error message at the beginning of the iterations) or Davidson Diagonalization (same convergence behaviour as mentioned above). I also use a very good guess (I have compared it with Molpro which takes so much less time and converges easily). Does anybody have any experience with this? Best regards, Ioannis From chemistry-request@server.ccl.net Wed Apr 3 10:28:45 2002 Received: from rwcrmhc53.attbi.com ([204.127.198.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33FSjp19064 for ; Wed, 3 Apr 2002 10:28:45 -0500 Received: from C1353359A ([12.228.114.158]) by rwcrmhc53.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020403152834.KMBW21252.rwcrmhc53.attbi.com@C1353359A>; Wed, 3 Apr 2002 15:28:34 +0000 Reply-To: From: "Mark Thompson" To: "Elmar Gerwalin" , Subject: RE: Semiempirical calc. of K with g98 ? Date: Wed, 3 Apr 2002 07:26:51 -0800 Message-ID: <000601c1db23$fa30e050$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Dear Elmar, You can add parameters to INDO1/s in ArgusLab via the external text-formatted zindo.prm file. You would have to come up with the parameters yourself, but it is feasible. ArgusLab is available at http://www.planaria-software.com/download_3_0.htm Mark ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.com ================================= > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On > Behalf Of Elmar Gerwalin > Sent: Wednesday, April 03, 2002 2:06 AM > To: CHEMISTRY@server.ccl.net > Subject: CCL:Semiempirical calc. of K with g98 ? > > > > Hello, > > I'd like to do semiempirical calculations containing K (potassium) > and would like to know which method (that's implemented in g98!) > is best > or > if it's possible to generate or add parameters for K to g98. > > ( I found from > http://www.chamotlabs.com/Freebies/Table/parameters-table.html > that INDO/1 parameters exist, but this is not available in g98 > ) > > Thanks for any help in advance! > > Bye > Elmar > > > ============================================================== > Elmar Gerwalin , University of Kaiserslautern, Germany > gerwalin@rhrk.uni-kl.de > (soon: ) http://www.rhrk.uni-kl.de/~gerwalin > ============================================================== > > > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Wed Apr 3 10:50:36 2002 Received: from dux1.tcd.ie ([134.226.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33Foap20264 for ; Wed, 3 Apr 2002 10:50:36 -0500 Received: from wallaceiwork (chy108098.phy.tcd.ie [134.226.108.98]) by dux1.tcd.ie (Postfix) with SMTP id 604EF629 for ; Wed, 3 Apr 2002 16:50:25 +0100 (IST) Message-ID: <003b01c1db27$ad99a660$626ce286@wallaceiwork> From: "Iain Wallace" To: "CCL" Subject: CCL: Gaussian 98 benchmarks Date: Wed, 3 Apr 2002 16:53:20 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0038_01C1DB30.0F536000" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0038_01C1DB30.0F536000 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi all,=20 I was wondering if any one could tell me where I could get some = benchmarks for G98 1) Intel pentium dual processor machines 2) IBM Sp/2 using Linda Ideally it would have a few sample files. I want to run a few test jobs = to make sure that my version of=20 gaussian is installed properly. Does any one have any optimisation tips = for compiling it ?=20 Also, does any one know if there is a utility program that will tell you = how many basis functions a particular molecule will have without running a job in Gaussian? Or is there a way = of getting gaussian just to output=20 the number of basis but not to run any calculations?=20 Thanks a million for all your help=20 Iain=20 ------=_NextPart_000_0038_01C1DB30.0F536000 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi all,
 
I was wondering if any one could tell = me where I=20 could get some benchmarks for G98
1) Intel pentium dual processor=20 machines
2) IBM Sp/2 using Linda
 
Ideally it would have a few sample = files. I want to=20 run a few test jobs  to make sure that my version of
gaussian is installed properly. Does = any one have=20 any optimisation tips for compiling it ?
 
Also, does any one know if there is a = utility=20 program that will tell you how many basis functions a = particular
molecule will have without running a = job in=20 Gaussian? Or is there a way of getting gaussian just to output =
the number of basis but not to run any=20 calculations?
 
 
Thanks a million for all your help =
 
Iain
 
------=_NextPart_000_0038_01C1DB30.0F536000-- From chemistry-request@server.ccl.net Wed Apr 3 12:37:25 2002 Received: from cse.nd.edu ([129.74.25.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33HbPp24292 for ; Wed, 3 Apr 2002 12:37:25 -0500 Received: from dylan.cse.nd.edu (ako@dylan.cse.nd.edu [129.74.32.170]) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id g33HbJh06922 for ; Wed, 3 Apr 2002 12:37:19 -0500 (EST) Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.11.2/8.10.1) with ESMTP id g33HbGa12903 for ; Wed, 3 Apr 2002 12:37:16 -0500 (EST) Date: Wed, 3 Apr 2002 12:37:16 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: CHARMM missing coordinates Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have a pdb file with only oxygen atoms. I used hbuild to create the hydrogen atoms to create a water box. But in the final pdb file, all the hydrogen atoms have 9999 as the coordinates. Any idea on how to correct that? Thanks Alice From chemistry-request@server.ccl.net Wed Apr 3 12:39:14 2002 Received: from MAIL.hsc.wvu.edu ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g33HdEp24347 for ; Wed, 3 Apr 2002 12:39:14 -0500 Received: from HSC-DOM4-Message_Server by MAIL.hsc.wvu.edu with Novell_GroupWise; Wed, 03 Apr 2002 12:39:41 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 5.5.5.1 Date: Wed, 03 Apr 2002 12:39:24 -0500 From: "Sue Heavner" To: Subject: convergence of MD simulations Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g33HdEp24348 Dear CCL members: I read that in NVE simulations, the ratio of RMS fluctuations of the potential and kinetic energies is an indication of convergence of energy, with RMS(PE)/RMS(KE) = 0.01 indicating a satisfactory level of global energy stabilization. Is there such a test for NTP simulations? Thanks in advance, Sue Heavner From chemistry-request@server.ccl.net Wed Apr 3 12:56:30 2002 Received: from nori.rl.ac.uk ([130.246.135.154]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33HuTp24790 for ; Wed, 3 Apr 2002 12:56:30 -0500 Received: from kohn.nd.rl.ac.uk.nd.rl.ac.uk (kohn.nd.rl.ac.uk [130.246.48.218]) by nori.rl.ac.uk (8.11.1/8.11.1) with ESMTP id g33Hu9V01493; Wed, 3 Apr 2002 18:56:15 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15531.16953.867937.992101@kohn.nd.rl.ac.uk> Date: Wed, 3 Apr 2002 18:56:09 +0100 To: "Sue Heavner" Cc: Subject: CCL:convergence of MD simulations In-Reply-To: References: X-Mailer: VM 7.03-rfhacked under 21.4 (patch 4) "Artificial Intelligence" XEmacs Lucid From: "Keith Refson" Sue Heavner writes: > Dear CCL members: > I read that in NVE simulations, the ratio of RMS fluctuations of > the potential and kinetic energies is an indication > of convergence of energy, with RMS(PE)/RMS(KE) = 0.01 indicating a > satisfactory level of global energy stabilization. Is there such a > test for NTP simulations? If you are using a Hamiltonian-derived set of equations for the NTP simulation (such as Nose/Parrinello-Rahman or Nose/Andersen) then the answer is yes -- just use the conserved Hamiltonian in place of the energy. Note that you can't do this directly for the common Nose-Hoover formulation, though Frenkel and Smit (p139) suggest a way of reconstructing a conserved quantity with a little extra work in solving for the s variable. Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 446652 K.Refson@ F: 01235 445720 @rl.ac.uk From chemistry-request@server.ccl.net Wed Apr 3 11:39:27 2002 Received: from smtp.etang.com ([61.152.250.207]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g33GdQp22519 for ; Wed, 3 Apr 2002 11:39:27 -0500 Received: from pak3 (unknown [140.232.202.93]) by smtp.etang.com (Postfix) with ESMTP id 908951CC207B0; Thu, 4 Apr 2002 00:38:43 +0800 (CST) Message-ID: <003601c1db2d$ea779000$5dcae88c@pak3> From: "Ming Lei" To: "Zhangxd" , "Jeff Nauss" Cc: References: Subject: Re: CCL:how i can get detailed secondary structure from coordinate file? Date: Wed, 3 Apr 2002 11:37:55 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Wish DSSP is helpful. The stride is also recommanded! You can search them by means of google. I forget the website. Best, Ming ----- Original Message ----- From: "Zhangxd" To: "Jeff Nauss" Cc: Sent: Monday, February 04, 2002 5:56 PM Subject: CCL:how i can get detailed secondary structure from coordinate file? > Dear All, > during my research, i need the detailed information about secondary > structure of my biology system, i had its coordinate file, how i can get > its secondary structure information from this coordinate file? just like > the following: > Resi. 1 to Resi. 10 AlphaHelix > Resi. 15 to Resi. 25 BetaSheet > >.................. > >............... > > hopefully it should be a program can do this automatically. > i had tried VMD, it just gives the graph of secondary structure of > the sequence but not a detailed text information like the above sample. > > thanks in advance!!!! > > > > -= 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 > > > > >