From chemistry-request@ccl.net Thu Jun 20 00:08:59 1991 Date: Thu, 20 Jun 91 02:38:35 GMT From: Joe Leonard To: chemistry%ccl.net%apgea.army.mil@crdec7.apgea.army.mil Subject: LabVision posting Status: R We've had various forms of discussions regarding what's appropriate for posting to this bboard, but WHATEVER the concensus arrived at was, posting costs and providing a sales incentive pitch IS INAPPROPRIATE. Post it on a Commercial net, not this one... Joe Leonard Computational Chemist Stardent Computer jle@stardent.com P.S. Yes, I've been zinged in the past for what seemed too much like marketing, but this one makes my worst look rather good... From chemistry-request@ccl.net Thu Jun 20 03:51:55 1991 Date: Thu, 20 Jun 1991 09:34:56 +0200 From: Finn Drablos Subject: Re: Free-energy perturbation calcs of zinc<->peptide binding To: chemistry@ccl.net Status: R ================== >Hello to all AMBER gurus out there: > >I want to do a slow-growth free-energy perturbation calculation to estimate >the Gibbs free-energy change for the process zinc-ion + peptide -> peptide. > >I have parameterised the zinc-ion in AMBER 3.0A as an 'H-bonding' type >of atom ie. it has 10-12 well-depth and equilibrium bond distances with >all relevent donor atoms on the peptide (peptide C=O, carboxylate-O, >amine H2N's etc). In addition, it has a point-charge calculated by fitting >the electrostatic potential with MOPAC. Thus the Zn<->donor atom interaction >energy has two major sources (i) electrostatics and (ii) 10-12 well-depth. > (...) > >Any comments about the treatment of the zinc-ion <-> peptide binding ? > >Looking forward (I think) to some discussion .... > >---- >Alan Arnold | Phone: +61 62 68 8080 >Chem. Department,University College | ACSNET: apa@ccadfa.oz >Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb >CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV I am not an AMBER guru, but I have used Discover for some peptide/Zn simulations, and have a few comments. In general I think that most molecular mechanics programs do have problems with metal ions, and two important reasons for this are polarization effects and coordination. With a metal ion we introduce a strong point charge into the system. Well, not all ions should be handled as point charges, really. But at the current level of MM theory they are, in most cases. Anyway, this will introduce polarization effects in groups close to the ion. This is important, especially in dynamics simulations, as polarization is a dynamic property. But most MM programs don't include polarizability. I have heard that AMBER 4.0 includes polarization effects, but I don't know how they are represented in the forcefield (Any comments, out there?). But maybe you should try to get 4.0 before you start to do simulations. The other problem is coordination. Some ions like Ca++ don't care really, some like Ni++ are very sensitive, and Zn++ is somewhere in between. But the problem is that you really need to modify you forcefield in order to include coordination effects, see for example A. Vedani, J. Comp. Chem., 1986, 7, 701-710. And one last potential problem. I don't have the paper on AM1 parameters for Zn at hand, but at least the MNDO parameters where mainly estimated on the basis of organometallic compounds, like ZnEt2 and ZnMeI, and not complexed ions. So you should verify that the result is reasonable (compare the geometry to known X-ray structures) (More comments on this, out there?). But as you may have guessed, I ended up doing my computations (only minimization / simple dynamics) very much the same way as you have indicated. I didn't have much choice, did I ... But be careful when you interpret you results! Regards, Finn Drablos PHONE +47 7 997710 FAX +47 7 997708 MR Center, SINTEF UNIMED, drablos@marvin.mr.sintef.no N-7034 TRONDHEIM, NORWAY finn.drablos@sintef.no --------------------------------------------------------------- From chemistry-request@ccl.net Thu Jun 20 04:44:36 1991 Date: Thu, 20 Jun 91 03:54:17 EDT From: Michael A. Lee To: chemistry@ccl.net Subject: Commercial discussion again Status: RO Hello Chemistry enthusiasts. I apologize in advance for sending you mail on a suject on which you have already heard too much - commercial postings. If I recall correctly, Jan Labanowski forwarded the posting from LabVision which resulted in the objection by Joe Leonard (jle@stardent.com). Jan Labanowski executed his personal judgement on this matter and I think that should be good enough for us. He asked for a discussion on the subject of commercial postings earlier and he got it and digested it and arrived at his own guidlines. These were announced. Jan is a scientist who has taken part of his energies to create this list with the genuine intention of advancing science. SO ... CUT SOME SLACK, OK! This is one of the best lists that I have encountered and I am sure that Joe Leonard will agree with that. I also expect that Joe will agree that when a scientist takes his/her time to do administrative (explative) work, we should be supportive. I respect his and similar personal perspectives but retain my opinion that we should leave Jan with a wide margin of judgement in such matters. Mike Lee Physics Kent State From R0MIRA01@ULKYVM.bitnet Thu Jun 20 07:02:00 1991 Date: Thu, 20 Jun 91 07:08:40 EDT From: "R. Miranda" Subject: commercial postings To: "chemistry-request" Status: RO I agree with Mike Lee. In fact, owing to jkl's proper judgement on when to pass on commercials, I became aware of the LabV "special", and became quite interested. I would not (and will not) consider LabV at its "regular" price. (Stop and over to more productive thinking.) From chemistry-request@ccl.net Thu Jun 20 09:23:36 1991 Date: Thu, 20 Jun 91 8:05:01 EDT From: George R Famini To: chemistry%ccl.net@BRL.MIL Subject: Re: LabVision posting Status: RO I agree whole heartedly with Joe Leonard, posting of prices IS inappropriate for a Scientific list (isn't that what this is supposed to be? We've done real well lately, with a lot more science and a lot less advertizing (be it softaware (commercial) or psot-docs...). I had thought there was a set of general guidelines that stated prices would not be presented on this list. George Famini US Army CRDEC From chemistry-request@ccl.net Thu Jun 20 09:25:50 1991 Date: Thu, 20 Jun 91 08:28:01 -0400 From: zheng@retina.chem.psu.edu (Ya-Jun Zheng) Subject: More on: Free-energy perturbation calcs of zinc<->peptide binding Status: RO ================== >Hello to all AMBER gurus out there: > >I want to do a slow-growth free-energy perturbation calculation to estimate >the Gibbs free-energy change for the process zinc-ion + peptide -> peptide. > >I have parameterised the zinc-ion in AMBER 3.0A as an 'H-bonding' type >of atom ie. it has 10-12 well-depth and equilibrium bond distances with >all relevent donor atoms on the peptide (peptide C=O, carboxylate-O, >amine H2N's etc). In addition, it has a point-charge calculated by fitting >the electrostatic potential with MOPAC. Thus the Zn<->donor atom interaction >energy has two major sources (i) electrostatics and (ii) 10-12 well-depth. > (...) > >Any comments about the treatment of the zinc-ion <-> peptide binding ? > >Looking forward (I think) to some discussion .... > >---- >Alan Arnold | Phone: +61 62 68 8080 >Chem. Department,University College | ACSNET: apa@ccadfa.oz >Australian Defence Force Academy | UUCP: ...!seismo!munnari!ccadfa.oz!lpb >CANBERRA ACT 2600 Australia | ARPA: apa%ccadfa.oz@SEISMO.CSS.GOV I want to add one thing. Kenneth Merz developed a AMBER force field for Zn laterly. It works well for the compounds investigated. His approach is similar to Alan Arnold's. It would be very interesting to compare these two. By the way Could you post your parameters here? Ya-Jun Zheng Penn State University From chemistry-request@ccl.net Thu Jun 20 10:12:51 1991 Date: Thu, 20 Jun 91 06:48:04 PDT From: crc@iris64.biosym.COM (Clifford Randall Cannon) Subject: Re: LabVision (and all commercial) postings. To: chemistry@ccl.net Status: R If people are going to vote, then here's mine: commercial announcements that are clearly marked as such, SHORT, and TRUTHFUL are perfectly appropriate to this forum for pro- fessionals who are trying to produce new knowledge and results. We all need to know what tools are available to us so we can do NEW work, not repeat what has already been done. From jkl@ccl.net Thu Jun 20 10:19:59 1991 Date: Thu, 20 Jun 91 10:23:25 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: Re: Shake algorithm in C, anyone ? Status: R I (jkl@ccl.net) am forwarding this message to the list: ---------- Begin Forwarded Message ---------- >From reg@chem.UCSD.EDU Wed Jun 19 19:19:05 1991 Date: Wed, 19 Jun 91 16:20:20 PDT From: reg@chem.UCSD.EDU (Richard E. Gillilan) To: jkl@ccl.net Subject: Re: Shake algorithm in C, anyone ? I have a C version of SHAKE which was given to me by Ilan Benjamin (Chem. Dept. UC Santa Cruz). It's set up for use with Wilson group dynamics code but is well commented I think (I haven't used it yet). I'm sure Ilan would be happy to give you a copy. His email address is ilan@scib.ucsc.edu Just mention that I saw your request and sent you his address. Richard Gillilan Postgraduate Research Chemist UCSD reg@sdchemw2.ucsd.edu (619) 534-0290 ----------- End Forwarded Message ----------- From jkl@ccl.net Thu Jun 20 11:17:26 1991 Date: Thu, 20 Jun 91 11:20:51 -0400 From: jkl@ccl.net To: chemistry@ccl.net Subject: Re: CSD for RISC Sytem/6000 Status: R I am forwarding this question to the list: ---------- Begin Forwarded Message ---------- >From WIGHTWIG@sydvm1.vnet.ibm.com Thu Jun 20 09:26:56 1991 Date: Thu, 20 Jun 91 23:26:37 EST From: "Glenn Wightwick" To: chemistry-request@ccl.net Subject: CSD for RISC Sytem/6000 Does anybody know whether the Cambridge Structural Database (CSD) is available for the IBM RISC System/6000 workstation? Any information and assistance would be very much appreciated. Regards Glenn ----------- End Forwarded Message ----------- From chemistry-request@ccl.net Thu Jun 20 12:36:42 1991 Date: Thu, 20 Jun 91 11:07 CST From: "Mike Mitchell, UofH Chemistry, (713)-749-4229" Subject: Molecular Display Programs for RISC 6000? To: CHEMISTRY@ccl.net Status: R Netters- Does anyone know of cheap or free molecular display programs for the IBM RISC 6000 machines for academic use? I'm thinking of programs like MIDAS or MMS of PCMODEL, etc., etc. I'm also interested in displaying ouput, trajectories, etc. from the academic version of CHARMm. Thanks. Mike Mitchell mitchell@uhrcc2.crcc.uh.edu mitchell@uhrcc2.bitnet From chemistry-request@ccl.net Thu Jun 20 14:02:07 1991 Date: Thu, 20 Jun 91 13:42:42 GMT From: Joe Leonard To: chemistry%ccl.net%apgea.army.mil@crdec7.apgea.army.mil Subject: Commercial postings Status: R Ok, ok, I'll eat my previous posting... Granted, the "rules" for the bboard indicated that commercial postings were acceptable, but I assumed that mention of price/discount structure were not (being rather more business than science)... Sorry for uproar... Joe Leonard Computational Chemist jle@stardent.com From chemistry-request@ccl.net Thu Jun 20 14:04:58 1991 Date: Thu, 20 Jun 91 13:38:18 EDT From: rs0thp@rohmhaas.COM (Dr. Tom Pierce) Subject: RE: Molecular Display Programs for RISC 6000? To: CHEMISTRY@ccl.net Status: R RE> "Does anyone know of cheap or free molecular display programs for the >IBM RISC 6000 machines for academic use?" Mike Mitchell... I think that an academic can obtain a copy of MacroModel from Professor Clark Still at Columbia Univ. (sl$model@cuchem a bitnet address) This version runs on IBM Risc/6000 but for best 3D display, requires the IBM GL graphics card (oft called the 24 bit card). Tom Pierce rs0thp@rohmhaas.com From chemistry-request@ccl.net Thu Jun 20 14:29:01 1991 Date: Thu, 20 Jun 91 13:47:01 EDT From: SRIVASTAV%CWKLO.DECNET@cwjcc.INS.CWRU.EDU Subject: Commercial postings To: chemistry@ccl.net Status: R Since we are on a roll here I couldnt keep myself out. I tend to agree with Joe's last posting. We could have commercial announcements (for informative purposes) but without the price/sales pitch tag (business purposes). As scientists we do need information about latest software but anything other than that we should obtain directly from the company/firm (maybe the ad could list the contact ph number). Of course the listowner should have the last say in the matter. From chemistry-request@ccl.net Thu Jun 20 16:17:08 1991 Date: Thu, 20 Jun 91 12:53:01 PDT From: ross@zeno.mmwb.ucsf.EDU Subject: software announcements To: chemistry@ccl.net Status: R One thing I would like to see is user reviews of software, "commercial" and otherwise. This could include comparing different packages. Bill Ross From chemistry-request@ccl.net Thu Jun 20 16:20:41 1991 Date: Thu, 20 Jun 91 12:37:05 PDT From: crc@iris64.biosym.com (Clifford Randall Cannon) To: chemistry@ccl.net Subject: To Price or Not to Price? Status: R I can understand people being uncomfortable with prices being mentioned, but let's remember too that we are all sensitive to price, whether we are academic or commercial users. The second question (after "What can the software do?") is "How much does it cost?", in nearly every case. (The third ques- tion is, "What discount can you give me?"). And we are all busy. A listed price often tells a reader at once whether he/she should spend ANY time finding out more. Again, I ask readers: if the announcement is SHORT (so you can quickly ignore it if it doesn't interest you), truthful (obviously), and factually informative (not puffery or a knock on a competitor), what's the harm? Let's put our energy into making useful things happen, not editing the information flow. From jkl@ccl.net Thu Jun 20 16:53:08 1991 To: chemistry@ccl.net Subject: Commercial announcements Date: Thu, 20 Jun 91 16:56:26 EDT From: jkl@ccl.net Status: R Dear Subscribers to Comp.Chem.List I would like to ask for the end of discussion on Commercial Postings (Yes, I am a Stalinist Hitler). We had it before and it resulted in a set of rules which are described in the help file (to get help file for the list send a message: send help from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.bitnet). You might accuse me of making rules to suit myself but please be reminded that I do not work for any software company and do not intend to at the moment. If you want to send me flames, please direct them to my mailboxes: jkl@ccl.net or JKL@OHSTPY.BITNET I will appreciate your comments. However, the rules are the rules and I try not to break them. Believe it or not, they are a compromise from the previous discussion on this topic. Compromise means that everybody loses, but this is life. My posting of Commercial Adveritisement was in accord with the rules of the list and please give me a break... Jan Labanowski Your friendly Hitler jkl@ccl.net JKL@OHSTPY.BITNET chemistry-request@ccl.net From hsellers@ncsa.uiuc.edu Thu Jun 20 17:52:23 1991 Date: Thu, 20 Jun 91 16:50:03 CDT From: hsellers@ncsa.uiuc.edu (Harrell Sellers) To: mitchell@uhrcc2.crcc.uh.edu Status: R RS6000 molecular graphics In my group at the NCSA we have developed a program for quantum chemistry scientific visualization RS/6000 machines and IRIS workstations (anything running the 24 bit GL board). Our program is intended for quantum chemistry graphics, but, also makes very nice images of ball and stick molecules as well and could be used for making very high quality images of macromolecules. However, there is no provision for the display of trajectories, etc so our program may not be all that useful for you. Harrell Sellers hsellers@ncsa.uiuc.edu 217/333-2754 From chemistry-request@ccl.net Thu Jun 20 19:15:09 1991 Date: Thu, 20 Jun 1991 15:20:59 PDT From: "W. Todd Wipke" To: chemistry@ccl.net Subject: PC MicroSoft Word 5.0/5.5 style for Tetrahedron Comput. Methodol. Status: R From: MX%"wipke@SECS.UCSC.EDU" 20-JUN-1991 14:53:30.36 To: WIPKE CC: Subj: Re: MicroSoft Word 5.0 style for the PC From: "W. Todd Wipke" To: FAX0236@uoft02.utoledo.edu >From: "DOUGLAS A. SMITH" >To: wipke@SECS.UCSC.EDU > >Is there a MicroSoft WORD 5.5 (or 5.0) style file for the PC - I do not >use a MacIntosh. > Yes, on the fileserv@TCM.UCSC.EDU is INSTR.MSWORD_RTF (LIST INSTR will tell you what the fileserv has) which was created on the MAC and published in volume 2 No. 1. Just yesterday I read it in to Word for Windows and printed it out, it works fine on the PC under windows and correctly generates the proper format and provides the named TCM styles that appear in the back of each issue of TCM. Thus the MAC and PC both use the same style sheet which as an RTF file is e-mailable. To receive a copy of INSTR.MSWORD_RTF, snd a msg to fileserv@TCM.UCSC.EDU with the following line in the body of the message: SENDME INSTR.MSWORD_RTF (this is an ascii file readable by MS Word) SENDME INSTR.MAC_MSWORD (tells about the styles) Edit the msg when you receive it to take off the headers and save as MSWORD.RTF, then read it in using the convert capability in MS WORD 5.0 for RTF format (Rich Text Format) on the PC. The INSTR.MAC_MSWORD is also ascii and describes the various styles and how to use them. Using these styles means you can forget about spacing and formatting, it is all automatic. Unfortunately, I don't have any automatic bibliographic formatting system for use with MS Word, but one can take the output of REFFORM which is an ascii file with TCM ascii mark-up-language for emphasis, emboldening, etc, and write a series of macros to convert @i{ ... } to italics and @b{ ... } to bold. You then have BibTeX features for MS Word. I haven't explored the MS Word macro language, but anyone who wants to give it a try can develop macros that will convert some of the *.NTS files published in TCM disks which were output by REFFORM. -Todd Wipke Editor-in-Chief TCM From jkl@ccl.net Thu Jun 20 23:40:05 1991 To: chemistry@ccl.net Subject: Apology for Hitler Date: Thu, 20 Jun 91 23:43:29 EDT From: jkl@ccl.net Status: R I was reminded that signing myself as "Your friendly Hitler" at the end of my last message was offending to many people. To explain my intentions I meant: "Your friendly dictator". To assure you that I did not mean to offent anyone and that I know enough about history, let me tell you that the third of my parents' siblings perished during WWII and two members of my close family disappeared during Stalin times. Please flame me at my personal address: jkl@ccl.net, JKL@OHSTPY.BITNET if you feel such urge. Jan Labanowski jkl@ccl.net JKL@OHSTPY.BITNET