From chemistry-request@server.ccl.net Thu Nov 1 08:50:36 2001 Received: from sun2.ruf.uni-freiburg.de ([132.230.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1DoZB08409 for ; Thu, 1 Nov 2001 08:50:35 -0500 Received: from uni-freiburg.de (PC2-IR4.physchem.uni-freiburg.de [132.230.171.109]) by sun2.ruf.uni-freiburg.de (8.10.2+Sun/8.10.2) with ESMTP id fA19pO027731; Thu, 1 Nov 2001 10:51:24 +0100 (MET) Message-ID: <3BE11C03.4DAA7BEA@uni-freiburg.de> Date: Thu, 01 Nov 2001 10:55:15 +0100 From: Oliver Hucke X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: Wibke Sudholt , CHEMISTRY@ccl.net Subject: Re: CCL:Adding hydrogens References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Daer Wibke, I can recommend the application of WhatIf for placing hydrogens in a protein structure. WhatIf can search for a globally optimized hydrogen network, considering possible mistakes of side chain orientation in the X-ray structure. The method is described in Hooft, R.W.W., Sander, C., Vriend, G.: Proteins: Structure, Function, and Genetics 26(1996): 363-376 WhatIf is almost free. Have a look at http://www.cmbi.kun.nl/whatif/ Kind regards, Oliver Hucke ______________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: hucke@uni-freiburg.de ______________________________________ Wibke Sudholt wrote: > > Hello everybody, > > I am searching for free programs that are able to add hydrogens to a given > xyz or pdb structure (organic molecule, protein). It would be great if one > has some control over this process, e.g. at which atoms how many hydrogens > are attached. > > Many thanks for every help! > > Wibke Sudholt > University of California, San Diego > > -= 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 -- ______________________________________ Oliver Hucke Inst. fuer Physikalische Chemie II Universitaet Freiburg Albertstr. 23a D-79104 Freiburg Tel. : +49-761-203-5130 (/-6179) Fax. : +49-761-203-6189 email: hucke@uni-freiburg.de ______________________________________ From chemistry-request@server.ccl.net Thu Nov 1 10:12:07 2001 Received: from cliff.st-andrews.ac.uk (root@[138.251.140.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1FC7B09814 for ; Thu, 1 Nov 2001 10:12:07 -0500 Received: from edge.st-andrews.ac.uk (sdjp@edge [138.251.140.2]) by cliff.st-andrews.ac.uk (8.9.1a/8.9.1) with ESMTP id PAA08539 for ; Thu, 1 Nov 2001 15:15:08 GMT Received: from localhost (sdjp@localhost) by edge.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id PAA02207 for ; Thu, 1 Nov 2001 15:15:05 GMT Date: Thu, 1 Nov 2001 15:15:05 +0000 (GMT) From: Stuart Purdie X-Sender: sdjp@st-and.ac.uk To: chemistry@ccl.net Subject: Re: CCL:Gaussian calculation speed In-Reply-To: <01103117163901.00822@euklid> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 31 Oct 2001, Bernd Schubert wrote: > > Avoid the -X flag to hdparm: I have personally had a case > > of data loss with such setup. > > But without the -X flag you only enable to use dma-1 --> with a maximum > transferrate of 16 MB/s. Using the -X flag you enable Ultra-DMA (ATA-33 -- > -X34, ATA-66 -- -X66, etc.). Some types of disk's, notably those made by Western Digital, and some controllers, notably the older one made by Via, don't behave quite correctly with UDMA, and thus if you have a WD disk, or a VIA motherboard controller, avoid the -X flag. Otherwise, it aught to be Ok. From chemistry-request@server.ccl.net Thu Nov 1 09:03:33 2001 Received: from mail04.europe.csc.com ([194.133.99.131]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1E3SB08763 for ; Thu, 1 Nov 2001 09:03:28 -0500 Received: by mail04.europe.csc.com (8.8.8+Sun/SMI-SVR4) id KAA01441; Thu, 1 Nov 2001 10:04:02 GMT Received: from av-int.eu.csc.com (192.168.140.24) by CSCgw. ID xai001254; Thu, 1 Nov 01 10:03:50 GMT Received: from ukhx48.avecia.com (unverified) by av-is-sweeper.aveciais (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Thu, 1 Nov 2001 09:48:10 +0000 Received: by UKHX48 with Internet Mail Service (5.5.2653.19) id ; Thu, 1 Nov 2001 09:47:25 -0000 Message-ID: <67DFB9481700D111900E00805F59F861038D9858@UKHX14> From: Tackley Daniel R To: "Comp Chem Mailing List (E-mail)" Subject: G98W test job timings Date: Thu, 1 Nov 2001 09:47:24 -0000 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="windows-1252" Hi, Does anyone have (or know where I could find) timings with the associated machine spec. for the test jobs that come with Gaussian 98. I am specifically interested in those for G98W (rev A.11 if possible) but it would also be useful to compare the results with those from other machines. Thanks, Daniel -- Dr Daniel Tackley Computational Chemistry Group Avecia Manchester UK Email: daniel.tackley@avecia.com Telephone: +44 161 721 2541 From chemistry-request@server.ccl.net Thu Nov 1 09:37:46 2001 Received: from srv2.resnet.ohio-state.edu ([164.107.3.56]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA1EbkB09251 for ; Thu, 1 Nov 2001 09:37:46 -0500 Received: (qmail 49900 invoked by uid 1011); 1 Nov 2001 14:51:54 -0000 Received: from kiniu@mps.ohio-state.edu by srv2.resnet.ohio-state.edu with qmail-scanner-0.96 (. Clean. Processed in 0.014295 secs); 01 Nov 2001 14:51:54 -0000 Received: from rjot-84-236.resnet.ohio-state.edu (HELO wong) (164.107.84.236) by srv2.resnet.ohio-state.edu with SMTP; 1 Nov 2001 14:51:54 -0000 Message-ID: <004201c162e3$4d707b40$ec546ba4@255.resnet.ohiostate.edu> From: "Kiniu WONG \(Kin-Yiu\)" To: Cc: Subject: checkpoint files not compatible in Linux OS and UNIX OS??? Date: Thu, 1 Nov 2001 09:41:33 -0500 Organization: Physics, OSU 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 Dear all, I have encounterd a problem about Gaussian 98 that the checkpoint files in UNIX OS can't be used in Linux OS and vice versa (the output files are attached below). How can I solve the problem? I am new to the computational chemistry, any kind of information or suggestion would be helpful! Thank you very much in advance!! Best regards, Kiniu ---- Kiniu WONG (Kin-Yiu) Graduate Student Department of Physics The Ohio State University Primary Email: kiniu@mps.ohio-state.edu Permanent Email: kiniu@alumni.cuhk.net Using Unix's checkpoint file: ************************************************* Gaussian 98: DEC-AXP-OSF/1-G98RevA.7 11-Apr-1999 1-Nov-2001 ************************************************* %rwf=/usr/tmp/temp %int=/usr/tmp/temp %d2e=/usr/tmp/temp %scr=/usr/tmp/temp %chk=/usr/tmp/temp %Mem=400MB ---------------------------------------------------------------------- #P UHF/3-21G SCF=(Direct, MaxCycle=128, Symm) MaxDisk=3GB Geom=Checkpo int ---------------------------------------------------------------------- 1/29=2,38=1/1; 2//2; 3/5=5,11=2,25=1,30=1/1,2,3; 4/7=2,9=4/1; 5/5=2,7=128,15=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Thu Nov 1 22:18:46 2001, MaxMem= 52428800 cpu: 0.2 (Enter /usr/local/g98/l101.exe) ---- test ---- Z-Matrix taken from the checkpoint file: /usr/tmp/temp.chk Charge = 0 Multiplicity = 1 C Recover connectivity data from disk....................................... ............................ ********************************************* Gaussian 98: x86-Linux-G98RevA.9 19-Apr-2000 1-Nov-2001 ********************************************* %rwf=/usr/tmp/temp %int=/usr/tmp/temp %d2e=/usr/tmp/temp %scr=/usr/tmp/temp %chk=/usr/tmp/temp %Mem=400MB Bad file opened by FileIO: Unit=2 I= 2 FPrev=40960 FCur= 0. FileIO: IOper= 9 IFilNo(1)= 2 Len= 0 IPos= 0 Q= 1$ dumping /fiocom/, unit = 1 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Error termination in NtrErr: NtrErr Called from FileIO. (End of file) If use Linux checkpoint file instead: ************************************************* Gaussian 98: DEC-AXP-OSF/1-G98RevA.7 11-Apr-1999 1-Nov-2001 ************************************************* %rwf=/usr/tmp/temp %int=/usr/tmp/temp %d2e=/usr/tmp/temp %scr=/usr/tmp/temp %chk=/usr/tmp/temp %Mem=400MB (End of file) Already at the end of file, even no error message ********************************************* Gaussian 98: x86-Linux-G98RevA.9 19-Apr-2000 1-Nov-2001 ********************************************* %rwf=/usr/tmp/temp %int=/usr/tmp/temp %d2e=/usr/tmp/temp %scr=/usr/tmp/temp %chk=/usr/tmp/temp %Mem=400MB ---------------------------------------------------------------------- #P UHF/3-21G SCF=(Direct, MaxCycle=128, Symm) MaxDisk=3GB Geom=Checkpo int ---------------------------------------------------------------------- 1/29=2,38=1/1; 2/40=1/2; 3/5=5,11=2,25=1,30=1/1,2,3; 4/7=2,9=4/1; 5/5=2,7=128,15=2,32=1,38=4/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Thu Nov 1 22:23:35 2001, MaxMem= 52428800 cpu: 0.1 (Enter /usr/local/g98/l101.exe) ---- test ---- Z-Matrix taken from the checkpoint file: /usr/tmp/temp.chk Charge = 0 Multiplicity = 1 C Recover connectivity data from disk. ...................... ............................................. From chemistry-request@server.ccl.net Thu Nov 1 09:12:54 2001 Received: from femail27.sdc1.sfba.home.com ([24.254.60.17]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1ECrB08870 for ; Thu, 1 Nov 2001 09:12:53 -0500 Received: from C1353359A ([65.4.172.51]) by femail27.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011101063724.YOSZ17369.femail27.sdc1.sfba.home.com@C1353359A>; Wed, 31 Oct 2001 22:37:24 -0800 Message-ID: <005601c1629f$4324eca0$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: "Wibke Sudholt" , References: Subject: Re: CCL:Adding hydrogens Date: Wed, 31 Oct 2001 22:34:30 -0800 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 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Dear Wibke, ArgusLab will add hydrogens to an entire structure or to a subset of selected atoms. It will also selectively optimize the hydrogens (or any atoms in a selected subset) if you need. The program can be obtained from http://www.planaria-software.com It runs on Microsoft Windows operating systems and has a host of other great features including a great 3D molecule builder. Mark ------------------------------------------------------------------------- home page: http://members.home.net/markt158/ ----- Original Message ----- From: "Wibke Sudholt" To: Sent: Wednesday, October 31, 2001 7:14 PM Subject: CCL:Adding hydrogens > Hello everybody, > > I am searching for free programs that are able to add hydrogens to a given > xyz or pdb structure (organic molecule, protein). It would be great if one > has some control over this process, e.g. at which atoms how many hydrogens > are attached. > > Many thanks for every help! > > Wibke Sudholt > University of California, San Diego > > > -= 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 Thu Nov 1 08:55:42 2001 Received: from mel.ruc.dk ([130.225.220.27]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1DtfB08589 for ; Thu, 1 Nov 2001 08:55:41 -0500 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id OAA03889 for ; Thu, 1 Nov 2001 14:58:43 +0100 (MET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id KAA02093; Thu, 1 Nov 2001 10:14:36 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 1 Nov 01 10:40:57 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 1 Nov 01 10:39:30 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Borosy, Andras {Basi~Basel}" Date: Thu, 1 Nov 2001 10:39:13 +0100 Subject: Re: CCL:Woodward-Fieser Rules CC: chemistry@ccl.net X-Confirm-Reading-To: "Jens Spanget-Larsen" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <2368E9B617D@virgil.ruc.dk> Borosy, Andras: > Does anyone know a program for calculation (estimation) of maximum > wavelengths of UV absorption (lambda-max) by using Woodward-Fieser > Rules: Dear Andras, just a word of nomenclature. You seem to assume that lambda-max refers to the "maximum wavelength" of UV-absorption. I think that it is common usage to apply the symbol lambda-max for the wavelength that corresponds to the absorbance maximum of a band. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Cell-Phone: +45 2320 6246 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Thu Nov 1 12:39:23 2001 Received: from mail.kemi.dtu.dk ([130.225.67.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1HdMB12709 for ; Thu, 1 Nov 2001 12:39:22 -0500 Received: from ouabain.ok.dtu.dk (tr4.ok.dtu.dk [192.38.70.74]) by mail.kemi.dtu.dk (8.11.4/8.11.4) with ESMTP id fA1HgQ317793; Thu, 1 Nov 2001 18:42:26 +0100 Received: from localhost ([127.0.0.1] helo=tr4.ok.dtu.dk) by ouabain.ok.dtu.dk with esmtp (Exim 3.12 #1 (Debian)) id 15zLrD-0006mz-00; Thu, 01 Nov 2001 18:42:23 +0100 To: chemistry@ccl.net Cc: Stuart Purdie Subject: Re: CCL:Gaussian calculation speed In-reply-to: Your message of "Thu, 01 Nov 2001 15:15:05 GMT." Date: Thu, 01 Nov 2001 18:42:23 +0100 From: Malcolm Gillies Message-Id: > Some types of disk's, notably those made by Western Digital, and some > controllers, notably the older one made by Via, don't behave quite > correctly with UDMA, and thus if you have a WD disk, or a VIA > motherboard controller, avoid the -X flag. Otherwise, it aught to be Ok. What documentation I've seen (it's pretty thin) suggests the problem is confined to the VIA Apollo VP2 chipset. Check your /proc/pci to see what you have, e.g $ less /proc/pci [...] Bus 0, device 1, function 0: PCI bridge: VIA Technologies VT 82C598 Apollo MVP3 AGP (rev 0). Medium devsel. Master Capable. No bursts. Min Gnt=12. [...] Recent VIA chipsets should be fine. My machine uses the VIA Apollo MVP3 chipset (quite common on low-end PIII machines) and I've seen no problems in six months or so using -X. I'm running kernel version 2.2.19, and I did need to enable an 'experimental' configuration flag (CONFIG_BLK_DEV_VIA82C586) to make this work. However, I believe it should work out of the box for the 2.4 series. Here's a few webpages with some further information: http://www.linuxdoc.org/HOWTO/mini/Ultra-DMA.html http://lhd.datapower.com/db/dispdriver.php3?DISP?310 http://www.linux-ide.org/ [unfortunately the information in the Ultra-DMA mini-howto is a couple of years old, and partially out of date] Misbehaving drives should be automatically detected and blacklisted by the kernel. A (possibly out-of-date) list is included in the Ultra-DMA mini-HOWTO listed above. I have also seen patches to the 2.2 and 2.4 series for additional chipset and feature support (e.g. UDMA100) but I haven't looked into this. See http://www.lwn.net/2000/1102/a/ide.php3 cheers, Malcolm -- Malcolm Gillies Post-doctoral researcher Organic Chemistry, Dept Chemistry, Technical University of Denmark From chemistry-request@server.ccl.net Thu Nov 1 11:17:36 2001 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1GHaB11343 for ; Thu, 1 Nov 2001 11:17:36 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.33) id 15zKa0-00000q-00; Thu, 01 Nov 2001 17:20:32 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.33) id 15zKZz-0003qQ-00; Thu, 01 Nov 2001 17:20:31 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <004201c162e3$4d707b40$ec546ba4@255.resnet.ohiostate.edu> References: <004201c162e3$4d707b40$ec546ba4@255.resnet.ohiostate.edu> Date: Thu, 1 Nov 2001 17:20:26 +0100 To: "Kiniu WONG \(Kin-Yiu\)" From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:checkpoint files not compatible in Linux OS and UNIX OS??? Cc: chemistry@ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fA1GHaB11344 >Dear all, > > I have encounterd a problem about Gaussian 98 that the checkpoint files >in UNIX OS can't be used in Linux OS and vice versa (the output files are >attached below). How can I solve the problem? I am new to the >computational chemistry, any kind of information or suggestion would be >helpful! Thank you very much in advance!! > The best idea seems to use formatted checkpoint files for transfer between different machines (use formchk and friends). +---------------------------------+-------------------------------------+ | Prof. Christoph van Wüllen | Tele-Phone (+49) (0)30 314 27870 | | Technische Universität Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Straße des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+-------------------------------------+ -- From chemistry-request@server.ccl.net Thu Nov 1 17:57:07 2001 Received: from hschipaa.hsc.usf.edu ([131.247.16.97]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA1Mv7B18677 for ; Thu, 1 Nov 2001 17:57:07 -0500 Received: from hschipaa.hsc.usf.edu ([131.247.16.105]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with SMTP id SAA29204 for ; Thu, 1 Nov 2001 18:00:09 -0500 (EST) Message-ID: <3BE1D3F6.FD74FE01@mindless.com> Date: Thu, 01 Nov 2001 18:00:06 -0500 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: determining types of affinity Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, With everyone's help I have finally been able to use Autodock to dock a small molecule to my protein of interest. My question is how does one go about determining each ligand-preotein interaction that exists in the final docked conformation. e.g.. the such and such hydroxyl, hydrogen bonds with THR-132. Is there something in autodock that can shows the affinities that exists on a certain docking job, or is this just a matter of guestimations to what energies are involved with what structures. Thanks for your suggestions, David Smith From chemistry-request@server.ccl.net Thu Nov 1 16:28:44 2001 Received: from mail.axelero.hu ([195.228.240.83]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fA1LSfB16971 for ; Thu, 1 Nov 2001 16:28:42 -0500 Received: (qmail 1553 invoked from network); 1 Nov 2001 22:31:40 +0100 Received: from line-140-54.dial.matav.net (HELO cthulhu) (145.236.140.54) by mail.axelero.hu with SMTP; 1 Nov 2001 22:31:41 +0100 Message-ID: <005101c1631c$73c77490$0200a8c0@cthulhu> From: "Tamas Gunda" To: References: Subject: Re: CCL:Adding hydrogens Date: Thu, 1 Nov 2001 22:30:39 +0100 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 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Mol2Mol can do that (although it is not a free program): you can add all hydrogens automatically, or step-by-step manually, deciding how many hydrogens to be added in what geometry. See www.compuchem.com/mol2mol.htm best regards Tamas Gunda -------------------------------------- Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Academy of Sciences University of Debrecen, POBox 36 H-4010 Debrecen Hungary ----- Original Message ----- From: "Wibke Sudholt" To: Sent: Thursday, November 01, 2001 4:14 AM Subject: CCL:Adding hydrogens > Hello everybody, > > I am searching for free programs that are able to add hydrogens to a given > xyz or pdb structure (organic molecule, protein). It would be great if one > has some control over this process, e.g. at which atoms how many hydrogens > are attached. > > Many thanks for every help! > > Wibke Sudholt > University of California, San Diego > > > -= 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 Thu Nov 1 17:18:47 2001 Received: from mail.rpi.edu (root@[128.113.22.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1MIlB17431 for ; Thu, 1 Nov 2001 17:18:47 -0500 Received: from rpi.edu (exothermic-05.dynamic.rpi.edu [128.113.21.160]) by mail.rpi.edu (8.11.3/8.11.3) with ESMTP id fA1MLpp98880; Thu, 1 Nov 2001 17:21:51 -0500 Message-ID: <3BE1C996.D3996021@rpi.edu> Date: Thu, 01 Nov 2001 17:15:50 -0500 From: "Curt M. Breneman" X-Mailer: Mozilla 4.77 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, hayden@compchem.com, pnewton@compchem.com Subject: Chemical Computing Group (CCG) Excellence Awards for Orlando ACS Meeting Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, As Treasurer of the ACS Division of Computers in Chemistry, it's again my pleasure to announce that the Chemical Computing Group (CCG) Excellence Award program is seeking applicants for Graduate Student travel fellowships to the 2002 ACS National Meeting in Orlando, Florida. To be eligible for a CCG Excellence Award, you must be a graduate student in good standing and be presenting your work within the COMP program. Presentations may be either in oral or poster format. Winners will receive up to $1,150 in travel funding as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. Candidates may apply for the CCG Excellence award by submitting an extended (2-page) abstract of their poster or presentation to me along with a letter of support from their research advisor, a CV, and a personal statement. The awardees will be chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. The funds may be used to cover up to US $1,150 of the travel or on-site costs associated with attending one of the ACS National Meetings - in this case, the Spring 2001 National Meeting in Orlando, FL. (Note: To be considered for a CCG Excellence Award, your presentation must be submitted through the ACS OASys system prior to the appropriate symposium submission deadline - and these are fast approaching!.) Important: CCG Excellence Award applications must be received before 12/15/01. Winners will be announced by 1/15/02. Please submit application materials to: Prof. Curt M. Breneman Treasurer/ COMP Division RPI Department of Chemistry 110 8th St, Troy, NY 12180 USA From chemistry-request@server.ccl.net Thu Nov 1 17:20:15 2001 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA1MKFB17462 for ; Thu, 1 Nov 2001 17:20:15 -0500 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id fA1MQAP02661 for chemistry@ccl.net; Thu, 1 Nov 2001 14:26:10 -0800 Received: from jnauss1-pc.accelrys.com (jnauss1-pc.sd.accelrys.com [172.30.51.68]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id fA1MQAX02651 for ; Thu, 1 Nov 2001 14:26:10 -0800 Message-Id: <5.1.0.14.0.20011101140519.00ae9ec0@sparky2.sd.accelrys.com> X-Sender: jnauss@sparky2.sd.accelrys.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 01 Nov 2001 14:06:31 -0500 To: chemistry@ccl.net From: Jeff Nauss Subject: Accelrys Customer Training in January Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Accelrys Inc. will be holding eight customer-training workshops in the United States during the month of January 2002. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). For macromolecular modeling, the workshops "Introduction to Life Science Modeling with InsightII" and "Homology-Based Protein Design" will be offered twice in January. From January 8-11, the workshop pair will be held at the San Diego Supercomputer Center in San Diego, CA. The following week, January 15-18, the same workshops will be offered at the North Carolina Supercomputing Center, Research Triangle Park, NC. For rational drug design techniques, during the week of January 15-18, two Cerius2 workshops will be held at Rutgers University, New Brunswick, NJ. The "Introduction to Cerius2 for Life Sciences Workshop" will be followed by the "Small Molecule and Drug Design with Cerius2" workshop. Finally, Accelrys Inc. will be holding a pair of workshops focusing on NMR techniques at the SGI facility in Mt. View, CA. These workshops are currently the only NMR workshops scheduled in North America for 2002. The "Biomolecular NMR: Processing and Analysis Workshop" will be held January 22-23 and focuses on using FELIX. On January 24-25, the "Biomolecular NMR: Structure Determination Workshop" will be given. This course addresses the generation, refinement, and evaluation of structures based upon NMR data predominantly using NMR X-PLOR in Insight II and CNX. Fees for each 2-day course are $1000 commercial, $500 government, and $400 academic. However, register for two courses in the same week and receive a 25% discount for the second workshop. Registration is on-line at URL http://www.accelrys.com/training/lifesci/registration.php. Further detailed information about these and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/lifesci/schedule.html). Please do not hesitate to contact us should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 Chris Arzt 858-799-5340 -- Jeffrey L. Nauss, PhD Phone: (858) 799-5555 Life Science Customer Training Fax: (858) 799-5100 Accelrys E-mail: jnauss@accelrys.com 9685 Scranton Road http://www.accelrys.com/training/lifesci/ San Diego, CA 92121-3752 On June 1, MSI, Synopsys, Oxford Molecular, and GCG became Accelrys. Accelrys is a subsidiary of Pharmacopeia, Inc.