From chemistry-request@server.ccl.net Wed Feb 6 05:50:47 2002 Received: from mail.umu.se ([130.239.8.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g16Aokc07724 for ; Wed, 6 Feb 2002 05:50:47 -0500 Received: from Gudban (alikon2.medbio.umu.se [130.239.104.108]) by mail.umu.se (8.8.8/8.8.8) with SMTP id LAA28650 for ; Wed, 6 Feb 2002 11:50:34 +0100 (MET) Message-ID: <000c01c1aefc$e1b4d200$6c68ef82@medgenet.umu.se> From: "Alexei Kozlenkov" To: Subject: autodock3: binding of charged ligands to metalloenzyme. Date: Wed, 6 Feb 2002 11:56:07 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C1AF05.431484C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C1AF05.431484C0 Content-Type: text/plain; charset="windows-1251" Content-Transfer-Encoding: quoted-printable Dear All, I know a somewhat similar question has been posted before, but I could = not find any answers... I'm trying now to use Autodock to dock amino acid-derived inhibitors to = an enzyme containing (2+)metal ions Zn and Mg and I get the following = problem. The COO- group binds to metal ion VERY (unrealistically ) = strongly. I do not believe this is correct, especially because the = experimental data suggests that NH2 is the main binding group. We would = rather expect the COO- to stick into the solution. The interaction is = mainly electrostatic. I wonder if there is a way to take into account = the solvation of COO group, or any other way round this problem?=20 Also, is it OK to assign a full 2units-charge to Zn and Mg in protein, = or it is better to calculate their real charges toghether with their = protein ligands, for example with some quantum mechanical approach?=20 In general, I would appreciate any advice about use Autodock to model = interactions of ligands with Zn or Mg in metalloenzyme active sites.=20 If anybody had experience with Autodock / metalloenzymes, how good are = the results usually?=20 Regards, Alexey Kozlenkov Dept. Med. Genetics, Umea University, Umea, Sweden email: alexei.kozlenkov@medgenet.umu.se ------=_NextPart_000_0009_01C1AF05.431484C0 Content-Type: text/html; charset="windows-1251" Content-Transfer-Encoding: quoted-printable
Dear All,
 
I know a somewhat similar question has been posted before, = but I could=20 not find any answers...
 
I'm trying now to use Autodock to dock amino = acid-derived=20 inhibitors to an enzyme containing (2+)metal ions Zn and Mg and I = get the=20 following problem. The COO- group binds to metal ion VERY = (unrealistically )=20 strongly. I do not believe this is correct, especially because the = experimental=20 data suggests that NH2 is the main binding group. We would rather expect = the=20 COO- to stick into the solution. The interaction is mainly = electrostatic. I=20 wonder if there is a way to take into account the solvation = of COO=20 group, or any other way round this problem?
 
Also, is it OK to assign a full 2units-charge to Zn = and Mg in=20 protein, or it is better to calculate their real = charges toghether=20 with their protein ligands, for example with some quantum mechanical=20 approach? 
 
In general, I would appreciate any advice about use = Autodock=20 to model interactions of ligands with Zn or Mg in metalloenzyme active = sites.=20
If anybody had experience with Autodock /=20 metalloenzymes, how good are the results = usually? 
 
Regards,
 
Alexey Kozlenkov
Dept. Med. Genetics,
Umea University, Umea, Sweden
email: alexei.kozlenkov@medgene= t.umu.se
 
 
------=_NextPart_000_0009_01C1AF05.431484C0-- From chemistry-request@server.ccl.net Wed Feb 6 05:58:05 2002 Received: from smtp.263.net ([202.96.44.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g16Aw4c07837 for ; Wed, 6 Feb 2002 05:58:04 -0500 Received: from localhost (localhost [127.0.0.1]) by smtp.263.net (Postfix) with SMTP id D25181E303981 for ; Wed, 6 Feb 2002 18:56:18 +0800 (CST) Date: Tue, 5 Feb 2002 19:16:40 +0800 From: songyunlong To: "chemistry@ccl.net" Subject: Charmm22 force field for DNA Organization: smmu X-mailer: FoxMail 3.11 Release [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20020206105618.D25181E303981@smtp.263.net> Dear Computational Chemsitry Listers: Recently,I met with a difficult problem.I want to run a MCSS job to investigate the active site of a protein-DNA complex.However,the MCSS job requires the force field must be charmm22 force field. Then I assign the charmm22 force field to the protein-DNA complex,however,some nitrogen atoms of DNA,such as N3,N7, are not parameterized by charmm22 force field.I wonder whether DNA has been parameterized by charmm22 force field.In my opinion,as a famous macromolecular force field,CHARMM should have parmaterized for DNA as well as protein.How can I settle this problem? How can I parameterize DNA with charmm22 force field? Could you please kindly give me any suggestions on this problem? Best wishes to you! Song Yunlong,Ph.D ~~~~~~~~~~~~~~~~~~~~~~~~~~ Dept of med chem School of pharmacy Sec Mil Med Univ Guohe Road,325 Shanghai,200433 E-mail:songyunlong@263.net ~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Feb 6 01:24:09 2002 Received: from web21305.mail.yahoo.com ([216.136.129.141]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g166O8c01574 for ; Wed, 6 Feb 2002 01:24:09 -0500 Message-ID: <20020206062358.28267.qmail@web21305.mail.yahoo.com> Received: from [208.241.25.130] by web21305.mail.yahoo.com via HTTP; Tue, 05 Feb 2002 22:23:58 PST Date: Tue, 5 Feb 2002 22:23:58 -0800 (PST) From: Richard SMITH Subject: QSAR IC50 (SUMMARY and more questions) To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers: Thank you very much for your replies. As there were so many requests for the summary, I am sending the summary here. But this summary provokes me more questions. So I dont want to stop here. I would like to hear from you on the follwoing: Is there any rule of thumb on minimum, maximum, and ideal number of compounds required for a generating a statistically significant QSAR equation. Can we use all the compounds from the same cluster of compounds, (but the important features may not show up in the final equation, as they may be common to most of the compounds). Then how do we handle this? Or is it necessary that one should use a diverse set of compounds? I mean compounds from various clusters with varying IC50? I would like to hear from you more on this aspects. Enclosed please find the summary for my earlier query: --------------------- My query Dear Friends: I am trying to build QSAR using 17 compounds for which IC50 values are available. Do I need to use the IC50 as it is or should I take log(IC50) or -log(IC50). The values range from 10 to 100. I tried IC50 and log(IC50) using GFA. I am getting different QSAR equation. Could you please advice me on how to proceed. Thanks in advance. Smith ----------------------REPLIES------------- "C D'Silva" Mon, 4 Feb 2002 19:19:21 GMT Dear richard, you take the log (1/IC50) and plot it against your physicochemical parameter. Biological activity is always plotted on the y axis and the parameter on the x-axis (eg. Hammett or logP). If you get a linear plot the biological activity is dependent on one parameter. However it is more than often that the biological activity is dependent on two or more parameters If you get a parabolic plot then there will be a parameter that will be present to the power of 2: this is usually log p or TT. I enclose attachments to two papers on the topic. Best Wishes Claudius ------------------------------------ "quanph" Tue, 5 Feb 2002 09:28:18 +0700 Dear Richard SMITH, I 'm receive of you. Actually, I want to find the equation for you. I 'm studying QSArs, but I the same you in this field. your question "the reason why only logIC50 has to be used in the QSAR equation and not raw IC50 values", I think because logIC50 is linear than raw IC50 values and easy find QSAR equation. And the QSARS method classic only find QSAR equation > from multi regression. As I know ANN, Fuzzy Logic and GA in GFA solve non-linear equation, find good structure-activity relationships. You can to use logIC50 and raw IC50 values for QSARs. Phung Quan --------------------------- "Dave Young" Mon, 04 Feb 2002 09:51:13 -0500 Richard, It sounds like you have a difficult job. First of all, one order of magnitude isn't a very big spread by biochemical standards. Second, you only have a small number of compounds. Also, you didn't specify whether the IC50's were obtained from biochemical assays or cell culture assay, or whether kinetics indicate competitive inhibition. In any case, I would like to see you summarize the replies to your question on the CCl. Here are some things to consider. First of all, you expect to see docking energies proportional to Ki values from biochemical assays. This is a simple Ahhrenius relationship between energy and kinetics. Docking can show extremely reactive compounds to bind well. However, if the compound is so reactive that it binds to residues on the surface of the enzyme instead of just in the active site, then there may be no inhibitory effect in biochemical assays since so little of it was left to interact with the active site. 3D QSAR pharmacophore models are, to a first approximation, directly proportional to docking energies. Unfortunately, this isn't necessarily a rigorous relationship, since charge-charge interactions are much stronger than the interaction between hydrophobic groups. Also, hydrophobic, hydrophobic interactions are difficult to represent correctly, since they are important relative to the interaction between the hydrophobic group and a polar solvent, or cell cytoplasm in the case of biological systems. QSAR prediction of cell culture data becomes even more slippery. First of all, a compound that binds well in biohchemical assays may not be lipophillic enough to get through the cell wall if it must interact with an enzyme inside of the cell. Second, something that works in biochemical assays may be toxic to cells. It might even interact with some other enzyme, giving unpredictable results. The choice of target enzyme may be based on an incomplete knowledge of some biochemical assay, so inhibiting it may have unexpected side effects. In theory, a conventional QSAR equation can incorporate information > from docking, 3D QSAR, lipophillicity, and toxicity to predict cell culture results, assuming that some of the other things that could go wrong don't. You always prefer to work with a large amount of data, prefereably with activities spanning many orders of magnitude. Drug design work is a matter of very delicate balances. You want something that binds well in the active site, but isn't so reactive it doesn't bind elsewhere. You wan't it specific to one enzyme, but able to inhibit all serotypes. You want it lipophillic enough to be bioavailable, but if it is too lipophillic, the liver will remove it from the body too quickly. If kinetics don't show the competitive inhibition of the enzyme, then your problems increase by several orders of magnitude. I know you are probably already familiar with most of what I have written here, but it is good to stand back and examine all aspects of the problem before focusing in on the task of the day. There are a selection of commercial tools available to attack these problems, but there is always something you would like that the commercial software doesn't do. There are also some companies developing some interesting ideas for combating problems like bioavailability and resistance build-up. Unfortunately, I can't give details about the drug design tools my company has been developing in this forum, but you can find some public info at www.exegenicsinc.com Good luck with your project. ---------------------------------- Mon, 4 Feb 2002 08:37:31 -0200 (BDB) "antonio luiz oliveira de noronha" Hi About your QSAR question. In fact, as in the Dr. Kubiny book, it doesn't matter, you can use whatever unit you want. But You should be aware that, in log units, usually the IC50 behaves linearly, and if you are doing a linear regression is will work fine. If you don't take the log, don't expect the IC50 to behave linearly, so don't use a linear regression. You should use IC50's ranging 2 log units at least to have a good model. Also, assuming that your data behaves linearly, in log units or not, the equations will be different as they will reflect different values of IC50, and a different range of values, also. My advice is use -log, or, if you want use the straight data, use a program capable to recognize/deal with non linear data. Regards -------------------- Mon, 4 Feb 2002 09:52:54 +1100 Dave.Winkler@csiro.au Hi, Richard, You should generally use log IC50 if possible, as the linear free energy relationships on which QSAR is based relate the energetics of binding to the log of the equilibrium constant for binding ki (or something related to it such as IC50) delta G = -rt lnk -- Cheers, Dave ------------------------------------ 02 Feb 2002 12:14:21 PST "Alan Shusterman" log(IC50) and -log(IC50) are equivalent, right? You should get the same QSAR except the signs of the coefficients are reversed. As for IC50 vs. log(IC50), most people work with the latter (partly because it makes the data more linear). Of course, these will (should) give different QSAR. If logX gives a linear relationship another variable, then X by itself should give an exponential relationship. -Alan ------------------------------------- Sat, 2 Feb 2002 17:53:54 +0100 "Jeremy R. Greenwood" The way I see it (and I'm no expert) IC50 is a type of equilibium constant, and the log of IC50 is related to binding energy (deltaG=1.36*(logpKI) + c, in kcal/mol). Since the type of equations you are likely to build are linear, and related somehow to properties which are assumed additive and hopefully related to binding energies, you want logIC50. Hope this helps a little, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- ----------------- Sat, 02 Feb 2002 11:26:06 +0000 jmmckel@attglobal.net Which one makes the most sense from your point of view? How many predictors are you using? I would take all the various fits back to a common value, perhaps the raw IC50, and see where the error is the smallest.... John McKelvey ------------------------------------------------------------- __________________________________________________ Do You Yahoo!? Send FREE Valentine eCards with Yahoo! Greetings! http://greetings.yahoo.com From chemistry-request@server.ccl.net Wed Feb 6 10:29:14 2002 Received: from gandalf.cber.nih.gov ([128.231.52.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g16FTEc28081 for ; Wed, 6 Feb 2002 10:29:14 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id KAA68724; Wed, 6 Feb 2002 10:21:21 -0500 (EST) Date: Wed, 6 Feb 2002 10:21:21 -0500 From: Rick Venable To: songyunlong cc: "chemistry@ccl.net" Subject: Re: CCL:Charmm22 force field for DNA In-Reply-To: <20020206105618.D25181E303981@smtp.263.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 5 Feb 2002, songyunlong wrote: > Recently,I met with a difficult problem.I want to run a MCSS job to > investigate the active site of a protein-DNA complex.However,the > MCSS job requires the force field must be charmm22 force field. Then > I assign the charmm22 force field to the protein-DNA > complex,however,some nitrogen atoms of DNA,such as N3,N7, are not > parameterized by charmm22 force field.I wonder whether DNA has been > parameterized by charmm22 force field.In my opinion,as a famous > macromolecular force field,CHARMM should have parmaterized for DNA > as well as protein.How can I settle this problem? How can I > parameterize DNA with charmm22 force field? Could you please kindly > give me any suggestions on this problem? The latest versions of the CHARMM academic parameters can be found at http://www.pharmacy.umaryland.edu/~alex/research.html There is a specific protein:nucleic acid set of matched RTF and PARAM files for use in studies of this type; it has existed for some time, and has been distributed with CHARMM since about 1995. Note that "charmm22 force field" is often a minimum requirement; it refers in general to the introduction of an "all atom" force field, including non-polar (aliphatic, etc.) H atoms. Other force fields such as GROMACS omit these atoms, as did CHARMM prior to version 22. For MCSS calculations, you may wish to use the most recent version of the "prot_na" files, found at the above URL. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Wed Feb 6 17:37:40 2002 Received: from mail1.cc.huji.ac.il ([132.64.1.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g16Mbdc05194 for ; Wed, 6 Feb 2002 17:37:39 -0500 Received: from 127.0.0.1 (localhost.localdomain [127.0.0.1]) by mail1.cc.huji.ac.il (Postfix) with SMTP id 6154D3FEDB; Thu, 7 Feb 2002 00:37:27 +0200 (IST) Received: from pob.huji.ac.il (pob.huji.ac.il [132.64.1.8]) by mail1.cc.huji.ac.il (Postfix) with ESMTP id 2E3D43FE55; Thu, 7 Feb 2002 00:37:27 +0200 (IST) Received: from e0c6y4 (di3-23.dialin.huji.ac.il [132.64.13.23]) by pob.huji.ac.il (8.11.6/8.11.1) with SMTP id g16MbHH29162; Thu, 7 Feb 2002 00:37:22 +0200 (IST) Message-ID: <000201c1c55f$ea5b46e0$170d4084@e0c6y4> From: "boris gorelik" To: "Miroslava Cuperlovic-Culf" , "CCL" References: <009e01c1ad7f$27df9320$0c640a0a@oncoirmb> Subject: Re: CCL:Computer system requirements Date: Tue, 5 Mar 2002 22:39:02 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0108_01C1C496.8CC2CE00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 This is a multi-part message in MIME format. ------=_NextPart_000_0108_01C1C496.8CC2CE00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable This depends on what are you going to do: In the case that you want to = wright your ouwn programs, I think, PC with linux on it is much better = then SGI: (better cost/benefit ratio, especially cost/speed), but if you = want to use off-shell products (like Insight etc) you might prefer SGI = station Best regards,=20 Boris Gorelik,=20 Hebrew University of Jerusalem Israel ------=_NextPart_000_0108_01C1C496.8CC2CE00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
This depends on what are you going to = do: In the=20 case that you want to wright your ouwn programs, I think, PC with linux = on it is=20 much better then SGI: (better cost/benefit ratio, especially = cost/speed), but if=20 you want to use off-shell products (like Insight etc) you might prefer = SGI=20 station
 
Best regards,
Boris Gorelik,
Hebrew University of = Jerusalem
Israel
------=_NextPart_000_0108_01C1C496.8CC2CE00-- From chemistry-request@server.ccl.net Wed Feb 6 15:29:09 2002 Received: from owl.chem-eng.northwestern.edu (IDENT:root@[129.105.205.198]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g16KT9c03600 for ; Wed, 6 Feb 2002 15:29:09 -0500 Received: (from scott@localhost) by owl.chem-eng.northwestern.edu (8.11.2/8.11.2) id g16KStM15453; Wed, 6 Feb 2002 14:28:55 -0600 Message-Id: <200202062028.g16KStM15453@owl.chem-eng.northwestern.edu> X-Mailer: exmh version 2.2 06/23/2000 with nmh-1.0.4 To: chemistry@ccl.net Subject: sodium basis sets X-URL: http://broadbelt.chem-eng.northwestern.edu/~scott/ From: Scott McMillan Reply-To: Scott McMillan Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Date: Wed, 06 Feb 2002 14:28:55 -0600 Sender: scott@owl.chem-eng.northwestern.edu Hello, I am concerned that sodium only has one electron in the LANL2DZ basis set. I would like to explore the influence of this by using an all-electron basis for sodium while still using the LANL2DZ basis for the other atoms. Any suggestions on which sodium basis to use? I could always use a Pople style basis set, but I think that mixing Pople and Dunning basis sets in the same calculation probably isn't a good idea. So I'm looking for a Dunning-like all-electron basis that I can use for sodium. My understanding is the LANL2DZ basis uses a slightly modified DZ/D95 basis for the valence electrons. Of course I can't just use the D95 basis for sodium (Gaussian complains the basis set isn't defined for sodium and the EMSL basis set order form confirms it). The McLean/Chander basis sets were obtained in a similar manner to the D95 basis, so I suppose that may be the best choice. Any thoughts? Thanks, Scott -- Scott McMillan - smcmilla@northwestern.edu Institute for Environmental Catalysis Department of Chemical Engineering, Northwestern University http://broadbelt.chem-eng.northwestern.edu/~scott/ From chemistry-request@server.ccl.net Wed Feb 6 20:12:58 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g171Cwc11744 for ; Wed, 6 Feb 2002 20:12:58 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g171Cmc18787 for ; Wed, 6 Feb 2002 19:12:48 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id TAA08785 for chemistry@ccl.net; Wed, 6 Feb 2002 19:12:47 -0600 (CST) Date: Wed, 6 Feb 2002 19:12:47 -0600 From: John Stone To: chemistry@ccl.net Subject: Announce: VMD 1.7.2 (Windows-only GUI update) is available Message-ID: <20020206191246.A8776@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i Dear CCL, I'm happy to announce that we have released a small Windows-specific update to our molecular visualization package VMD, version 1.7.2. This update is only for the Windows platform, we suggest that Unix/Mac users should be running VMD 1.7.1 if they aren't already. During the course of our VMD 1.8 development efforts we fixed a deficiency in the implementation of the mouse cursor manipulation and event handling code for the VMD OpenGL window. The old behavior made resizing of the VMD OpenGL window tricky, and less pleasurable to use than the Unix/Mac versions, in that regard. Since the required code changes were small, I took the code from our VMD 1.8 development tree and back-patched it against VMD 1.7.1, so that we could bring this improvement to the users immediately, rather than waiting until VMD 1.8 goes through the full release cycle. If you're running VMD on Windows, I highly recommend upgrading to this new version. The rest of the code remains unchanged, so we're able to provide this new version with much less testing (and thus delay) than is usually required. VMD 1.8 development news: ------------------------- We're already well into developing VMD 1.8, and we have some great things in progress for that release. One of the highlights in VMD 1.8 will be the new "plugin" system which will allow extension modules to be added to VMD on-the-fly, without having to recompile the program. This is similar in principle to the plugins you may already be familiar with for web browsers. In the case of VMD, we intially used the plugin system as a means of providing the "psfgen" structure building interface in VMD 1.7.1 and 1.7.2. VMD 1.8 extends the plugin system significantly, and will use plugins for all file readers and writers, and will allow VMD users to write their own readers/writers for their favorite molecule file formats with much greater ease. This is particularly useful for those individuals developing their own simulation software that have need to make their own file formats. Since this plugin work is still in the fairly early stages, we have not yet written the full documentation that will ultimately be included when the functionality is complete, but we would be very interested in hearing from individuals that would like to develop file reader/writer plugins for VMD 1.8. The best part about plugins is that they may be distributed separately from VMD, and can be developed "after the fact" for already shipping versions of VMD (post 1.8). In this way, authors of an MD simulation package can provide a file reader/writer plugin for VMD with their simulation package, and know that VMD users will be able to read their program's data files. If you are interested in developing file reader/writer plugins, please do send us an email. Thanks! John Stone vmd@ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Wed Feb 6 20:41:35 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g171fZc12666 for ; Wed, 6 Feb 2002 20:41:35 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g171fPc19089 for ; Wed, 6 Feb 2002 19:41:25 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id TAA08846 for chemistry@ccl.net; Wed, 6 Feb 2002 19:41:24 -0600 (CST) Date: Wed, 6 Feb 2002 19:41:24 -0600 From: John Stone To: chemistry@ccl.net Subject: Re: Announce: VMD 1.7.2 (Windows-only GUI update) is available Message-ID: <20020206194123.A8820@geneseo.ks.uiuc.edu> References: <20020206191246.A8776@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <20020206191246.A8776@geneseo.ks.uiuc.edu> User-Agent: Mutt/1.3.19i Dear CCL, My apologies for sending a second message, but I belatedly realized that I forgot to include the URLs for the VMD web site. Since some readers may not be familiar with VMD yet, here are the pertinent URLs: VMD home page: http://www.ks.uiuc.edu/Research/vmd/ Download page: http://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD Thanks for your time. Enjoy, John Stone vmd@ks.uiuc.edu -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Wed Feb 6 21:37:27 2002 Received: from smtp.dicp.ac.cn ([159.226.159.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g172bQc14356 for ; Wed, 6 Feb 2002 21:37:27 -0500 Received: from congyao ([159.226.159.204]) by smtp.dicp.ac.cn (8.11.6/8.11.6) with SMTP id g172b8E11303 for ; Thu, 7 Feb 2002 10:37:11 +0800 Message-Id: <200202070237.g172b8E11303@smtp.dicp.ac.cn> Date: Thu, 7 Feb 2002 10:37:15 +0800 From: wangyanemail To: "chemistry@ccl.net" Subject: about conjuate gradient approach X-mailer: FoxMail 3.11 Release [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit CCLers: I know there is a method for fast transition state location in Dmol3.This method combines the classic linear and quadratic synchronous transit metnods with a conjuate gradient approach to refine the saddle point geometry. My question is how to refine the sassle point geometry with a conjuate gradient approach in Dmol3 .what is conjuate gradient approach. I cant find the option(conjuate gradient approach) in Dmol3. Any help is welcome. best regards wangyanemail wangyanemail@dicp.ac.cn