From chemistry-request@server.ccl.net Tue May 7 05:48:20 2002 Received: from relay1.softcomca.com ([168.144.1.67]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g479mJV18485 for ; Tue, 7 May 2002 05:48:20 -0400 Received: from m2w037 ([168.144.108.37]) by relay1.softcomca.com with Microsoft SMTPSVC(5.0.2195.4905); Tue, 7 May 2002 05:48:19 -0400 X-Originating-IP: 202.185.72.119 X-URL: http://www.mail2web.com/ Subject: Autodock result not consistent with crystal structure Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Tue, 7 May 2002 05:48:19 -0400 To: "chemistry@ccl.net" Reply-To: nepenthes@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-ID: X-OriginalArrivalTime: 07 May 2002 09:48:19.0396 (UTC) FILETIME=[51856040:01C1F5AC] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id g479mKV18486 Hi CCLers, I'd like to hear from anybody who's used Autodock regarding the results I'm getting. I docked a ligand which was taken out of a crystalized ligand-protein complex and used it to dock into the binding site. I tested with rigid docking and it works well but when the ligand is flexible, I got a whole lots of conformations which don't really produce the crystalized binding mode very well. At most one 3 or 4 conformations only will have better conformations (compare to the crystal structure), with different binding affinity. Whatever the case, the lowest binding affinity calculated is still found in the binding site, just that the frequency of this conformation is not high. I don't quite understand why this happened, aside from the fact maybe the force field wasn't suitable ( I used CVFF) or maybe the ligand has different binding modes. The total charge on my protein is negative while the ligand is positive. Does anybody have this sort of problem or am I just not using Autodock correctly. I tried many times with changing some parameters but the results are pretty much consistent. Any feedback will be truly appreciated. Thanks. Rowyna K. -------------------------------------------------------------------- mail2web - Check your email from the web at http://mail2web.com/ . From chemistry-request@server.ccl.net Tue May 7 08:34:55 2002 Received: from dux1.tcd.ie ([134.226.1.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47CYtV21607 for ; Tue, 7 May 2002 08:34:55 -0400 Received: from wallaceiwork (chy108098.phy.tcd.ie [134.226.108.98]) by dux1.tcd.ie (Postfix) with SMTP id A41227EA for ; Tue, 7 May 2002 13:34:47 +0100 (IST) Message-ID: <000a01c1f5c4$3b17dfa0$626ce286@wallaceiwork> From: "Iain Wallace" To: "CCL" Subject: CCL: Gaussian on a dual intel pentium Date: Tue, 7 May 2002 13:39:29 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01C1F5CC.9CCB7EC0" 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_0007_01C1F5CC.9CCB7EC0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, I am about to install G98 A7 on a dual pentium IV machine with linux 7.2 = . I was wondering if any one could tell me=20 what I compiler switches will provide me with the best performance for a = dual processor machine, using the portland compiler.=20 Thanks=20 Iain=20 ------=_NextPart_000_0007_01C1F5CC.9CCB7EC0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

I am about to install G98 A7 on a dual = pentium IV=20 machine with linux 7.2 . I was wondering if any one could tell me =

what I compiler switches will provide = me with the=20 best performance for a dual processor machine, using the portland = compiler.=20

Thanks

Iain

------=_NextPart_000_0007_01C1F5CC.9CCB7EC0-- From chemistry-request@server.ccl.net Tue May 7 06:46:57 2002 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47AkuV19424 for ; Tue, 7 May 2002 06:46:56 -0400 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Tue, 7 May 2002 12:46:52 +0200 Received: from werkman.bmc.uu.se (werkman.bmc.uu.se [130.238.37.169]) by XRAY.bmc.uu.se (8.11.6/8.8.7) with ESMTP id g47ApD113626 for ; Tue, 7 May 2002 12:51:13 +0200 Date: Tue, 7 May 2002 12:34:32 +0200 (CEST) From: David van der Spoel X-X-Sender: cc: "chemistry@ccl.net" Subject: Re: CCL:Autodock result not consistent with crystal structure In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 7 May 2002, nepenthes@vplaces.net wrote: >I'd like to hear from anybody who's used Autodock regarding the results >I'm getting. I docked a ligand which was taken out of a crystalized >ligand-protein complex and used it to dock into the binding site. I >tested with rigid docking and it works well but when the ligand is >flexible, I got a whole lots of conformations which don't really produce >the crystalized binding mode very well. At most one 3 or 4 conformations >only will have better conformations (compare to the crystal structure), >with different binding affinity. Whatever the case, the lowest binding >affinity calculated is still found in the binding site, just that the >frequency of this conformation is not high. > >I don't quite understand why this happened, aside from the fact maybe >the force field wasn't suitable ( I used CVFF) or maybe the ligand has >different binding modes. The total charge on my protein is negative while >the ligand is positive. Does anybody have this sort of problem or am I >just not using Autodock correctly. I tried many times with changing some >parameters but the results are pretty much consistent. There are two points to consider: force field accuracy and searching efficiency. Rigid docking is easier on the searching algorithm, so if you find the pocket there it means it can be found. However this is no guarantee that a flexible ligand would find the same site, even with infinite searching, since a flexible ligand might find other (lower) energy minima. I have a paper coming up in Protein Science about the efficiency of docking using Autodock. We basically found that we could reproduce most crystal complexes (8 out of 10) with flexible ligands. It may need some parameter tuning (e.g. larger population size), however, and quite a bit of patience because some of these dockings took several 100 hours of CPU time. -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Tue May 7 12:45:46 2002 Received: from ns1.tudelft.nl ([130.161.180.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47GjkV28421 for ; Tue, 7 May 2002 12:45:46 -0400 X-Confirm-reading-to: zwijnenburg@stm-ltc2.stm.tudelft.nl X-PMrqc: 1 Received: from CONVERSION-DAEMON.mailhost2.tudelft.nl by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) id <0GVR002012K2RX@mailhost2.tudelft.nl> for chemistry@ccl.net; Tue, 07 May 2002 18:45:40 +0200 (MEST) Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost2.tudelft.nl (PMDF V6.0-025 #40925) with ESMTP id <0GVR00JDY2K2DG@mailhost2.tudelft.nl> for chemistry@ccl.net; Tue, 07 May 2002 18:45:38 +0200 (MEST) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g47Gjb327441 for ; Tue, 07 May 2002 18:45:37 +0200 (MEST) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Tue, 07 May 2002 18:45:38 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Tue, 07 May 2002 18:45:34 +0000 (MET-1MEST) Date: Tue, 07 May 2002 18:45:33 +0200 From: Martijn Zwijnenburg Subject: G98 convergence criteria To: chemistry@ccl.net Message-id: <3CD820CC.21760.F6A106@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal Hi, Does anybody know, or know where to find, to which convergence criteria the keywords (tight, verytight, no keyword (standard) and sleazy) correspond. I don't seem to find in the manual. Regards, Martijn Zwijnenburg ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Tue May 7 14:02:22 2002 Received: from kineo.bowdoin.edu ([139.140.14.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47I2MV30985 for ; Tue, 7 May 2002 14:02:22 -0400 Received: from [139.140.135.25] ([139.140.135.25]) by kineo.bowdoin.edu (Netscape Messaging Server 4.15) with ESMTP id GVR63X00.RDU; Tue, 7 May 2002 14:02:21 -0400 User-Agent: Microsoft-Entourage/10.0.0.1309 Date: Tue, 07 May 2002 14:02:20 -0400 Subject: Re: CCL:G98 convergence criteria From: "Ha-Yeon Cheong" To: Martijn Zwijnenburg , Message-ID: In-Reply-To: <3CD820CC.21760.F6A106@localhost> Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit On 5/7/02 12:45 PM, "Martijn Zwijnenburg" wrote: > Hi, > > Does anybody know, or know where to find, to which convergence > criteria the keywords (tight, verytight, no keyword (standard) and > sleazy) correspond. I don't seem to find in the manual. > > Regards, > > Martijn Zwijnenburg > ------------------------------------------------------------------------- > Martijn Zwijnenburg > Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology > Julianalaan 136 > 2628 BL Delft > The Netherlands > Tel: 0031-(0)152782691 > Fax: 0031-(0)152784700 > e-mail: M.A.Zwijnenburg@tnw.tudelft.nl > web page: http://come.to/tock > > -= 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 > > > > > > Dear Martijn Zwijnenburg, What you are looking for is the convergence criteria of the keyword OPT. I am saying this because there are two difference convergence criteria in gaussian98. One is in keyword SCF, and the second is in OPT. You are right, they are not listed in the manual or the gaussian website, but you can find out rather quickly by running a quick optimization with both criteria. Gaussian outputs the criteria in its logfile. It doesn't matter what method you use. Just run HF level STO-3G basis set with OPT=TIGHT or OPT=VERYTIGHT. And then 'grep' or look for these four things for the individual criteria: "Maximum Force" "RMS Force" "Maximum Displacement" "RMS Displacement" It's painless and more exact than anybody's memory. Cheers. HYC From chemistry-request@server.ccl.net Tue May 7 14:19:44 2002 Received: from front1.chartermi.net ([24.213.60.123]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47IJhV31238 for ; Tue, 7 May 2002 14:19:43 -0400 Received: from [24.247.80.10] (HELO hppav) by front1.chartermi.net (CommuniGate Pro SMTP 3.5.3) with SMTP id 97539114 for CHEMISTRY@ccl.net; Tue, 07 May 2002 14:19:43 -0400 Message-ID: <000b01c1f5f3$c2c47ec0$0201a8c0@hppav> From: "Jim Kress" To: Subject: Kinetic (or Dynamic) Monte Carlo Date: Tue, 7 May 2002 14:19:43 -0400 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 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Anybody know where I could get a good Kinetic (or Dynamic) Monte Carlo program? Preferably free. Thanks. Jim From chemistry-request@server.ccl.net Tue May 7 12:11:08 2002 Received: from hotmail.com ([64.4.37.220]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47GB8V27153 for ; Tue, 7 May 2002 12:11:08 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 7 May 2002 09:11:02 -0700 Received: from 171.64.127.133 by pv2fd.pav2.hotmail.msn.com with HTTP; Tue, 07 May 2002 16:11:02 GMT X-Originating-IP: [171.64.127.133] From: "Bin Shan" To: chemistry@ccl.net Subject: How to place a charge using CHARGE keyword in Gaussian98 Date: Tue, 07 May 2002 16:11:02 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 07 May 2002 16:11:02.0891 (UTC) FILETIME=[C8D4A3B0:01C1F5E1] I am trying to simulate the electric field by point charge and need to place the charge in an appropriate position relative to the molecule.I have difficulty trying to do this. # hf/6-31G(d) Charge Title section 0 1 molecule specification ... -10.000000 0.000000 17.320508 7.0 It is the last line that arises the difficulty.As my specification for the molecule is always in Z-matrix format,I do not know whether there is a convenient way to place the charge relative to my molecule(say,I want to it be 4.0A from atom1 and makes an angle 90 with atom1 and atom2 and a dihydral angle of 90 with atom1 and atom2 and atom3) > From Gaussian website: By default, the charges are read from the input stream, one per line, in this format: x y z charge point charge format So if I specify the molecule in Z-matrix format,I do not know how it is converted to cartesian coordinate and how the charge is placed relative to the molecule.If I were to use cartesian coordinate for the molecule,it is not very easy to specify the charge position relative to some certain atoms.I am wondering if there is a good way of doing that.Hope someone can help me out. _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. From chemistry-request@server.ccl.net Tue May 7 12:56:27 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47GuRV28641 for ; Tue, 7 May 2002 12:56:27 -0400 Received: from eden.rutgers.edu (unknown [165.230.180.178]) by goshen.rutgers.edu (Postfix) with ESMTP id 85B371FA5B for ; Tue, 7 May 2002 12:56:27 -0400 (EDT) Received: from eden.rutgers.edu (pool2-192.envsci.rutgers.edu [165.230.172.192]) by eden.rutgers.edu (Postfix) with ESMTP id D62801648F for ; Tue, 7 May 2002 12:56:26 -0400 (EDT) Message-ID: <3CD8099C.E6BEAC1A@eden.rutgers.edu> Date: Tue, 07 May 2002 13:06:36 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Force fields Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLer's: First of all, I want to thank everyone who has ever helped me in the past. CCL was a great help to me in finishing my doctoral research, and getting my degree.So, is anyone needs a computational chemist in the field of environmental science...(shameless self promotion). My question is-does anyone have any references on how to go about constructing force fields? I would need detailed references that explain the process "from scratch". As always, your help is greatly appreciated. Mary V. O'Connor, Ph.D. Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Tue May 7 13:28:40 2002 Received: from mo.schrodinger.com ([192.156.98.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47HSdV30250 for ; Tue, 7 May 2002 13:28:39 -0400 Received: from localhost (jshelley@localhost) by mo.schrodinger.com (SGI-8.9.3/8.9.3) with ESMTP id KAA83905 for ; Tue, 7 May 2002 10:28:30 -0700 (PDT) X-Authentication-Warning: mo.schrodinger.com: jshelley owned process doing -bs Date: Tue, 7 May 2002 10:28:30 -0700 From: John Shelley To: CHEMISTRY@ccl.net Subject: Summary: Disk solutions in heterogeneous environments Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, There were 3 very helpful responses to my query about cheap disk-storage that can cross mounted on a wide variety of Unix platforms. They are listed below (with permission for responses not already posted to the list). Looks like this can work with some care (kernel problems for which patches are available seem to be the key). I really appreciate the responses provided, John Shelley Senior Scientist Schrodinger, Inc --------------------- Original Question: Dear CCL, I'm curious about a cheap relatively modest disk solution (100-500 GBytes) that can be effectively cross mounted on a wide variety of unix systems (Linux, SUN, AIX, HP, Compaq TRU64 and SGI IRIX) using NFS for scientific data storage/access. It need not be a RAID system but could be. The main reason that I'm asking about this is that I've heard about severe problems with access to the disk being frequently frozen with simultaneously cross mounting relatively cheaps disks in heterogeneous environments using NFS. I'd appreciate any success/problem stories that people might have regarding this issue. ================================ Here are the answers received: ================================ From: Jim Phillips We've been using Sun servers running Solaris, mounted by all of those platforms, stably for years. (Actually, we just got the AIX box last week, but everything else has been working solidly for three years.) You can get a low-end Sun for $1000. We've had bad luck with Linux servers. - - - - - - - The computer systems used in the Theoretical Biophysics Group, Computing Facility an NIH Resource for Macromolecular Modeling and Bioinformatics are described at: http://www.ks.uiuc.edu/Development/Computers/ or http://www.ks.uiuc.edu/Development/Computers/systems.html ================================ From: Malcolm Gillies Hi John, I'm not sure I understand what you're looking for, but we have a Linux NFS server which is mounted by a cluster of 15 Linux machines, as well as a couple of SGIs. All very simple and cheap, and no problems since it was installed about 18 months ago. The disks themselves are SCSI, but I can't see that IDE would make a big difference, apart from SCSI being easier to swap around (we have fancy rackmount enclosures). A couple of weeks ago I set up software RAID on a Linux machine for the scratch partition (hoping to speed up the I/O). That went very easily using the Red Hat install tools, and so far nothing unusual has popped up. That's not being served across NFS of course. What do you mean by "relatively cheap disks"? With regard to "freezing", I have had two problems with poor response times across NFS on my Linux machines. The first was simply due to loading the server with CPU intensive processes (eg jaguar), which was easily solved by keeping those jobs off the server. The second was due to a bug in the Ethernet driver on the client machine, which was causing extremely low network throughput. Fixed with a kernel upgrade, once I realized what was going on. - - - - - - - Follow-up messages: > > What do you mean by "relatively cheap disks"? Somewhere in between business class RAIDs with very high reliability and disks commonly used on PCs. > > [...] > the various machines that we need to work on. We have had some problems > with large cheap disks and cross mounting them from Linux to a lot of > other computers. I've heard that the disk would go into a weird state > (NFS problem) and that would essentially make it inaccessible on all the > computers. Inaccessible is a mild term since doing a df would cause the > window involved to irreversibly lock up as well. Do you have anything to go on suggesting that the problem was disk- related rather than purely NFS-related? (Not really but perhaps kernel related, I was not involved in this.) As someone else mentioned, having a dud kernel version can be a problem. Particularly with older kernels (pre 2.2.14, from memory) the NFS implementation had some serious problems. Our NFS server is running an SGI-patched 2.2 series kernel which apparently includes some NFS fixes. I believe these and many more are included in the current 2.4 series releases. NFS3 over UDP appears to be the preferred option at the moment; the TCP implementation is still flaky. If you want something off the shelf, there are various Linux-based boxes around, like the Cobalt Qube gear (sold by Sun these days?). More expensive than rolling your own, of course. ======================================== This one was posted on CCL From: Szilveszter Juhos For a Linux/BSD based solution go for hardware RAID(5) with a reliable card ( http://linas.org/linux/raid.html ). You can use NFS automounter (for Linux sometimes better to use the BSD-based daemon instead of the kernel automounter). Also NFS 3 client/server is supported for Linux nowadays. If you are using many inodes/files, it is adviced to increase /proc/sys/fs/file-max (2.4 kernel and also the inode-max on 2.2. kernels) to its double/triple value. Also better to use the vm33 patch on a machine that is used as an application server (though it is always a bad idea to give the fileserver into the users hand ;) Do not forget that for automounted volumes you have to explicitly 'cd' into the dir, it is not enough to use the auto-completion in the shell (the TAB key I mean). Adviced to use a journalling filesystem BUT NOT reiserfs on such systems. ext3/xfs is the option, I do not know how IBM's jfs is performing, but that also can be an option. Backing up such data is a pain if you do not want to pay for expensive tape robots, etc. People say amanda (GNU) is OK, I have very good experiences with arkeia (that is not free for this size unfortunatelly but still many times cheaper than Veritas or HSM solutions). Also due to the frequent RPC vulnerabilities better to have at least a packet filter firewall. So there is no out-of-the box Linux solution, but with some tuning you can have a pretty good system. I was managing ~2TB on-line data with similar architecture in a heterogenous net (Linux,HP,Solaris,Windows,IRIX). The main source of problems was cr@py hardware RAID cards and out-of-the-box kernels. From chemistry-request@server.ccl.net Tue May 7 15:25:19 2002 Received: from qtp.ufl.edu ([128.227.89.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47JPJV32748 for ; Tue, 7 May 2002 15:25:19 -0400 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1/deumens) with SMTP id PAA26556; Tue, 7 May 2002 15:25:20 -0400 (EDT) Message-ID: <021001c1f5fd$f70d9cc0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Bin Shan" Cc: "CCL - all" References: Subject: Re: CCL:How to place a charge using CHARGE keyword in Gaussian98 Date: Tue, 7 May 2002 15:32:41 -0400 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 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Dear Bin, last time I did use charges (G94), they were placed at the point specified in the input (I think in units of bohr). Then the molecule gets rotated and shifted into the standard orientation. If you optimize, your atoms move, but not the charge. If you want to place the charge at a specific point with respect to your molecule, you may add a He-atom to your geometry specification, run a short calc (e.g. with %kill l301 1; I'm not sure about the syntax anymore. It should kill the calc after link 301 finishes for the first time.) and convert the cartesian coordinates of the dummy to bohrs. In order to prevent the center-of-mass shift caused by the He, you need to: 1) Get cartesian coords for your molecule from the last "standard orientation" of the optimization. 2) Add the He in z-matrix style. Use the "no-reorient" or "no-symm" options to prevent reorientation of the molecule in the next calc (use %kill). 3) get the cartesian coords of the He, convert them to bohrs and use that coordinate for the charge you want to place. Since I'm somewhat out of practice with Gaussian, the actual keywords may differ a little. Sorry for that. Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu University of Florida | (352) 392-6714 Quantum Theory Project 2341 NPB #92, P.O.Box 117200 Gainesville, FL 32611-7200 From chemistry-request@server.ccl.net Tue May 7 19:48:14 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g47NmEV06210 for ; Tue, 7 May 2002 19:48:14 -0400 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g47NmAjD032444 for ; Tue, 7 May 2002 16:48:10 -0700 Received: FROM dante35.u.washington.edu BY mailscan-out1.cac.washington.edu ; Tue May 07 16:48:10 2002 -0700 Received: from localhost (jzheng73@localhost) by dante35.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g47NmAnH063008 for ; Tue, 7 May 2002 16:48:10 -0700 Date: Tue, 7 May 2002 16:48:10 -0700 (PDT) From: "J. Zheng" cc: chemistry@ccl.net Subject: charmm MAXIMUM error In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer: Now I am trying to practice a few examples which are provided on website http://www.psc.edu/general/software/packages/charmm/tutorial/crowley /protein_index.html. I use example "Snake venom peptide from Green Mamba Snake". When I take the second step, i.e. Minimization and solvation , the CHARMM gives following ERROR MESSEAGE. -------------------------------------------------------------------------- **** ERROR **** A COUNTER VARIABLE HAS EXCEEDED ITS MAXIMUM ALLOWABLE VALUE. EXECUTION WILL BE TERMINATED. THE CURRENT COUNTER VARIABLES AND THEIR MAXIMUM ALLOWED VALUES ARE: NSEG = 37 MAXSEG = 1000 NATOM = 25296 MAXA = 25140 NBOND = 25316 MAXB =25140 NTHETA = 11323 MAXT = 25140 NPHI = 5183 MAXP = 50280 NIMPHI = 351 MAXIMP = 9200 NNB = 0 MAXNB = 17200 NDON = 271 MAXPAD = 8160 NACC = 7962 MAXPAD = 8160 NRES = 7905 MAXRES = 14000 NATC = 99 MAXATC = 500 NCB =138 MAXCB = 1500 NCT = 341 MAXCT = 15500 NCP = 443 MAXCP = 3000 NCI = 46 MAXCI = 600 --------------------------------------------------------------------------- It shows that NATOM and NBOND has exceeded its maximum value. Anyone can give me suggestion to fix this problem. I will appreciate for your help. Jie From chemistry-request@server.ccl.net Tue May 7 20:52:10 2002 Received: from mailer.psc.edu ([128.182.58.100]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g480qAV08530 for ; Tue, 7 May 2002 20:52:10 -0400 Received: from pscuxc.psc.edu (pscuxc.psc.edu [128.182.66.177]) by mailer.psc.edu (8.11.2/8.11.2/psc) with ESMTP id g480q8h26490; Tue, 7 May 2002 20:52:08 -0400 (EDT) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.9.3/8.9.3/psc) with ESMTP id UAA00446; Tue, 7 May 2002 20:52:08 -0400 (EDT) Date: Tue, 7 May 2002 20:52:08 -0400 (EDT) From: Troy Wymore To: "J. Zheng" cc: Subject: Re: CCL:charmm MAXIMUM error In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Jie, It looks like you probably compiled the medium version of CHARMM or at least that's what you are using. You can compile a large version that will take care of the problem. $ ./install.com large You can look into the file install.com to see what are the available options for machine type, etc. Good luck, Troy Wymore Biomedical Initiative Group Pittsburgh Supercomputing Center On Tue, 7 May 2002, J. Zheng wrote: > > Dear CCLer: > > Now I am trying to practice a few examples which are provided on website > http://www.psc.edu/general/software/packages/charmm/tutorial/crowley > /protein_index.html. > > I use example "Snake venom peptide from Green Mamba Snake". When I take > the second step, i.e. Minimization and solvation , the CHARMM gives > following ERROR MESSEAGE. > > -------------------------------------------------------------------------- > **** ERROR **** A COUNTER VARIABLE HAS EXCEEDED ITS MAXIMUM ALLOWABLE > VALUE. EXECUTION WILL BE TERMINATED. > THE CURRENT COUNTER VARIABLES AND THEIR MAXIMUM ALLOWED VALUES ARE: > > NSEG = 37 MAXSEG = 1000 NATOM = 25296 MAXA = 25140 > NBOND = 25316 MAXB =25140 NTHETA = 11323 MAXT = 25140 > NPHI = 5183 MAXP = 50280 NIMPHI = 351 MAXIMP = 9200 > NNB = 0 MAXNB = 17200 NDON = 271 MAXPAD = 8160 > NACC = 7962 MAXPAD = 8160 NRES = 7905 MAXRES = 14000 > NATC = 99 MAXATC = 500 NCB =138 MAXCB = 1500 > NCT = 341 MAXCT = 15500 NCP = 443 MAXCP = 3000 > NCI = 46 MAXCI = 600 > --------------------------------------------------------------------------- > > It shows that NATOM and NBOND has exceeded its maximum value. > > Anyone can give me suggestion to fix this problem. > > I will appreciate for your help. > > Jie > > > > -= 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 > > > > > >