From chemistry-request@server.ccl.net Wed Jul 17 05:34:59 2002 Received: from dove2.cf.ac.uk ([131.251.1.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6H9Ywv18302 for ; Wed, 17 Jul 2002 05:34:58 -0400 Received: from thor.cf.ac.uk ([131.251.0.1]) by dove2.cf.ac.uk with esmtp (Exim 3.03 #2) id 17UlCs-0003Lo-00; Wed, 17 Jul 2002 10:34:50 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id KAA17464; Wed, 17 Jul 2002 10:34:50 +0100 (BST) Date: Wed, 17 Jul 2002 10:34:47 +0100 (BST) From: Jamie Platts X-Sender: sacjap@thor To: Stephen Bowlus cc: "'chemistry@ccl.net'" Subject: Re: CCL:MOLVOL In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Stephen - we've got the Fortran77 source for MOLVOL, which I'll send separately. My student has also modified it to read MDL mol files, rather than the original xyz format - would you prefer that? Cheers, Jamie ---------------------------------------------------------- Jamie Platts Dept. of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts@cf.ac.uk P.O. Box 912 FAX: +44 (0) 2920 874030 Cardiff CF10 3TB www.cf.ac.uk/chemy On Tue, 16 Jul 2002, Stephen Bowlus wrote: > Does anyone know how or from whom one can obtain the program MOLVOL by Dodd > and Theodorou? I have been unable to locate a repository for the program, > or Prof. Dodd, who seems to be (have been?) its curator. > > Thanks in advance for suggestions, > Steve > > *************************************************************** > Stephen B. Bowlus, Ph.D. > Senior Computational Scientist > > LION bioscience, Inc. Stephen.Bowlus@lionbioscience.com > 9880 Campus Point Dr. Phone: (858) 410-6542 > San Diego, CA 92121 Fax: (858) 410-6665 > *************************************************************** > > > > From chemistry-request@server.ccl.net Wed Jul 17 07:08:08 2002 Received: from noralf.uib.no ([129.177.30.12]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HB87v19866 for ; Wed, 17 Jul 2002 07:08:07 -0400 Received: from nkjtk.kj.uib.no [129.177.52.113] by noralf.uib.no with esmtp (Exim 3.35) id 17Umet-0000G1-00; Wed, 17 Jul 2002 13:07:51 +0200 Message-Id: <5.0.2.1.2.20020717105209.009f8d60@rasmus.uib.no> X-Sender: st06087@rasmus.uib.no X-Mailer: QUALCOMM Windows Eudora Version 5.0.2 Date: Wed, 17 Jul 2002 12:17:22 +0200 To: chemistry@ccl.net From: Shireen Al Falah Subject: ROMP4 using gaussian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-checked-clean: by exiscan on noralf X-Scanner: 7c842943f242f7cf2addd9072b6b45df http://tjinfo.uib.no/virus.html X-UiB-SpamFlag: NO UIB: -7 hits, 8 required; Hi to ccl users, I need to run a ROMP4 using gaussian98. I have tried to do it. But I was no lucky. Do you know a way to do it. The same input file with the keyword ROMP2 worked. Can you explain the reason for that, please The input is as follows: %mem=30000000 %nproc=4 %chk=et_bht_p_ROMP4 #P ROMP4/gen SP Vshift=300 gfinput IOP(6/7=3) scf=(tight,novaracc,maxcycle=300) pop=Full units=Ang Guess=Cards The error message is: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. #P ROMP4/GEN SP VSHIFT=300 GFINPUT IOP(6/ ' Last state="GCL" TCursr= 827 LCursr= 3 Error termination via Lnk1e in /usr/local/chemistry/g98/l1.exe. Best regards, Sherin Alfalah From chemistry-request@server.ccl.net Wed Jul 17 07:08:16 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HB8Gv19884 for ; Wed, 17 Jul 2002 07:08:16 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g6HB8GqX028452 for ; Wed, 17 Jul 2002 08:08:16 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Wed Jul 17 08:08:15 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id IAA26932 for ; Wed, 17 Jul 2002 08:08:15 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Wed, 17 Jul 2002 08:08:15 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: Answers to Number of Atom Types in Autodock Message-ID: <3D3526F1@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" X-Mailer: WebMail (Hydra) SMTP v3.61.08 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g6HB8Gv19885 Thank you to everyone who responded to my question. I have managed to recompile Autodock and Autogrid under Linux using the autocomm.h-extra-maps to replace the original autocomm.h in both Autodock and Autogrid. So now I should have up to 15 atom types available for docking calculations. Note: I tried compiling on my SGI, but the GNU GCC compiler on SGI didn't really like the "make" file, therefore I switched to Linux, which compiled with minimal problems. Below is my original question and the responses. Thanks again to everyone, Robert Original Question: Fellow CCLers, A question on Autodock and the number of atom types allowed in the ligand used for docking. My ligand contains Carbon, Aromatics, Nitrogen, Oxygen, Sulphur, Hydrogens, and Fluorine atoms. Apparently Autodock allows only 7 atom types. When I try to run the docking with this particular ligand, I get the following error message: autodock3: ERROR: ERROR: 7 atom types declared in "", S_line "CANOSHF"; maximum allowed is 6. Change "ATOM_MAPS" in "autocomm.h" autodock3: Aborting... autodock3: Unsuccessful Completion. I found two "autocomm.h" files, and also another called autocomm.h-extra-maps, however changing the contents of the autocomm.h files did not correct the problem. My questions are: 1- Can autodock support more than 6 different atom types per ligand 2- Am I going to have to recompile Autodock in order to be able to use ligands with more than 6 atom types. I will post the answers to the board. Thank you in advance. Robert REPLIES: Hi Rob, did you recompile the code...? i have autodock with up to 15 atomtypes. if you need help to compile or modify the code please email me and i will send you a patch file. you need to modify both autodock and autogrid. its best to hack the files in the src/autodock/autocomm.h and the same for autogrid respectively i did the following #define MAX_MAPS 16 /* Maximum number of energy maps */ #define ATOM_MAPS 14 /* Number of atomic affinity grids */ #define NATOMTYPES 15 /* Number of atom types for atomic interactions */ #define MAX_TYPES 8 /* Maximum number of atom types used. */ then do a make and a make install cheers Kim ************************************************************ I solved this problem by re-compiling autodock. The change required is in the file autocomm.h: change line: #define ATOM_MAPS 6 to be: #define ATOM_MAPS 8 (or however many you need) It sounds like you made this change to autocomm.h already. What is then required is to re-compile the program by typing the command "make". Susan Heffron P.S. In my particular case, on an SGI, I had to make the following changes to the Makefile to get it to run without error messages: old line: OLIMIT = $(CSTD) $(OPT) # SGI, Sun, HP, Convex, >... new line: OLIMIT = $(CSTD) $(OPT) -OPT:Olimit=2442 # Some SGIs. old line: DBUG = -DNDEBUG # No debugging and no assert code. new line: DBUG = # Use assert code. ========================================================================== Thanks, Susan Heffron **************************************** Hi Rob, I have had the same problem. Infact, htis problem has been discussed about two weeks ago in CCL. To answer your questions: 1.No 2.Yes, but you d have to change a great deal of source code, which was, at least for me, beyond my capabilities of programming. I talked to the guys of SCRIPPS and they said it would take some efford to allow more than six atom types, infact they know about this problem. I couldn t figure out why they didnt allow lets say ten types right away. Apart from that, AutoDock works really well. Hope this helps. Carsten ~~~~~~~~~~~~~~~~~~~~~~~~~~~ Carsten Detering University of Washington Seattle, WA 98195 email detering@u.washington.edu ~~~~~~~~~~~~~~~~~~~~~~~~~~~ I solved this problem by re-compiling autodock. The change required is in the file autocomm.h: change line: #define ATOM_MAPS 6 to be: #define ATOM_MAPS 8 (or however many you need) It sounds like you made this change to autocomm.h already. What is then required is to re-compile the program by typing the command "make". Susan Heffron P.S. In my particular case, on an SGI, I had to make the following changes to the Makefile to get it to run without error messages: change: OLIMIT = $(CSTD) $(OPT) # SGI, Sun, HP, Convex, ... to be: OLIMIT = $(CSTD) $(OPT) -OPT:Olimit=2442 # Some SGIs. change: DBUG = -DNDEBUG # No debugging and no assert code. to be: DBUG = # Use assert code. -- ------------------------------------------------------------------ Susan Heffron Dept. of Physiology and Biophysics University of California, Irvine Irvine, CA 92697-4560 U.S.A. phone: (949) 824-4625 FAX: (949) 824-8540 ------------------------------------------------------------------ In general, a program must be recompiled whenever changes are made to any of the *.h files; these are part of the source code. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** From chemistry-request@server.ccl.net Wed Jul 17 08:58:39 2002 Received: from kbtfw.kubota.co.jp (firewall-user@[133.253.102.202]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HCwbv21651 for ; Wed, 17 Jul 2002 08:58:38 -0400 Received: by kbtfw.kubota.co.jp; id g6HCwZq20115; Wed, 17 Jul 2002 21:58:36 +0900 (JST) Received: from unknown(133.253.122.4) by kbtfw.kubota.co.jp via smap (V5.0) id xma020064; Wed, 17 Jul 02 21:58:13 +0900 Received: from kubotaj.tt.kubota.co.jp (kbtgk.eto.kubota.co.jp [133.253.122.3]) by kbtmk.eto.kubota.co.jp (8.12.2/8.12.2) with ESMTP id g6HCvo1v044965 for ; Wed, 17 Jul 2002 21:58:03 +0900 (JST) Received: from tt.kubota.co.jp (pegasus.tt.kubota.co.jp [133.253.130.15]) by kubotaj.tt.kubota.co.jp (8.9.3+3.2W/3.7W) with ESMTP id VAA29810 for ; Wed, 17 Jul 2002 21:58:38 +0900 Received: from muramasa01.kubota.co.jp [133.253.130.200] by tt.kubota.co.jp (SMTPD32-7.06) id AB0E10BA009A; Wed, 17 Jul 2002 22:03:10 +0900 Message-Id: <10207171255.AA00003@muramasa01.kubota.co.jp> From: atsutoshi konoo Date: Wed, 17 Jul 2002 21:55:48 +0900 To: chemistry@ccl.net Subject: anyone tell me how to build g98 A11 with ifc 6.0 X-ALMail-Regist: Request to license MIME-Version: 1.0 X-Mailer: AL-Mail 1.34 Content-Type: text/plain; charset=us-ascii hi CCLers I am trouble about compiling Gaussian98 Rev A11 with Intel Fortran Compiler. Please tell me how to build it with properly. It's first compilation g98 with ifc for me. I am using ifc(intel fortran compiler)6.0 evaluate version,and it works good. for building with ifc,I modified some part of bsd/i386.make like as following. RUNF77 = ifc F2CLIB = LIBS = -lPEPCF90 UNROLL = -unroll VECTOR = -vec TWOH = PC64 = -pc64 and I got build.logs like as below -------bldg98.log------------------------- . . . . rm ./as8zmYLF.as rm ./argt9fLkg.arg rm -f ml0.f ml0.c make[1]: Leaving directory `/home/g98' ifc -O2 -tp p6 -unroll -vec -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -W0 -v -o g98 ml0.o util.so -lPEPCF90 ifc: warning: -vec is default; use -x and -ax to configure vectorization ld \ /usr/lib/crt1.o \ /usr/lib/crti.o \ /opt/intel/compiler60/ia32/lib/crtxi.o \ -dynamic-linker \ /lib/ld-linux.so.2 \ -o \ g98 \ ml0.o \ util.so \ -lPEPCF90 \ -Qy \ /opt/intel/compiler60/ia32/lib/icrt.link \ -u \ ___pseudo_link \ -L/opt/intel/compiler60/ia32/lib \ -L/usr/lib \ -Bstatic \ -lintrins \ -lIEPCF90 \ -lF90 \ -lintrins \ -limf \ -Bdynamic \ -lm \ -Bstatic \ -lirc \ -Bdynamic \ -lcxa \ -Bstatic \ -lcprts \ -lunwind \ -Bdynamic \ -lcxa \ -Bdynamic \ -lc \ /opt/intel/compiler60/ia32/lib/crtxn.o \ /usr/lib/crtn.o util.so: undefined reference to `wait_' util.so: undefined reference to `fork_' make: *** [g98] Error 1 ------------------------------------------ comparing to pgf77 building logs,I found wait_ and fork_ is linked pgf77 libs. if when one use ifc,which libraries must be required? or,Does anyone know website which has informations about g98 built with ifc? finally,I am sorry for my silly question. regards. ################################# KGT Inc systerm service dept cluster tech group Atsutoshi Konoo +81-03-3225-0747 a-konoo@kubota.co.jp ################################# -- atsutoshi konoo a-konoo@kubota.co.jp From chemistry-request@server.ccl.net Wed Jul 17 01:57:55 2002 Received: from sccrmhc02.attbi.com ([204.127.202.62]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6H5vtv15435 for ; Wed, 17 Jul 2002 01:57:55 -0400 Received: from C1353359A ([12.228.8.181]) by sccrmhc02.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with SMTP id <20020717055750.REFD6023.sccrmhc02.attbi.com@C1353359A>; Wed, 17 Jul 2002 05:57:50 +0000 Reply-To: From: "Mark Thompson" To: Subject: ArgusLab 3.1 release available ! Date: Tue, 16 Jul 2002 22:59:18 -0700 Message-ID: <000101c22d57$16a59430$0300a8c0@attbi.com> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 ************************************************************* ArgusLab version 3.1 now available Download a full-featured trial version at: http://www.arguslab.com ************************************************************* New features added: 1. Improved interface in the molecule builder 2. Improved for automatically adding bonds 3. Export images to bitmap, JPEG, and TIFF file formats 4. Export POV-Ray image files. (spectacular ray-traced images) 5. Improved Help System with more Tutorials and FAQs 6. Improved "clean geometry" will un-flatten rings 7. Full control over Atom colors 8. Enter explicit coordinates for atoms from right-click menu 9. Modify bond lengths from right-click menu 10. Reads older PDB file formats. 11. Lots of bug fixes. ArgusLab features: Extensive support for rendering surfaces. Powerful 3D interactive molecule builder. Build and optimize structures for the entire periodic table. Support for spectroscopy, geometry optimizations, energies, and many properties. ================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA. http://www.arguslab.com ================================= From chemistry-request@server.ccl.net Wed Jul 17 10:05:46 2002 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HE5jv23085 for ; Wed, 17 Jul 2002 10:05:45 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.36) id 17UpQy-0001fV-00; Wed, 17 Jul 2002 16:05:40 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.36) id 17UpQx-00017h-00; Wed, 17 Jul 2002 16:05:39 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <10207171255.AA00003@muramasa01.kubota.co.jp> References: <10207171255.AA00003@muramasa01.kubota.co.jp> Date: Wed, 17 Jul 2002 16:05:38 +0200 To: atsutoshi konoo From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:anyone tell me how to build g98 A11 with ifc 6.0 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 g6HE5kv23086 >hi CCLers > > >I am trouble about compiling Gaussian98 Rev A11 with Intel Fortran >Compiler. >Please tell me how to build it with properly. >It's first compilation g98 with ifc for me. > if wait_ and fork_ are not included in the ifc libs (Try -Vaxlib), then it is trivial to write a "wrapper" in C (its a one-liner). Wait and Fork are simply FORTRAN-callable versions of the well-known wait() and fork() system calls (look at rs6kdum.F and mdutil.F for hints). Probably you can use dummies for the first try. I guess that fork() and wait() are only used in parallel calculations. +---------------------------------+----------------------------------+ | 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 Wed Jul 17 10:36:32 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HEaWv23966 for ; Wed, 17 Jul 2002 10:36:32 -0400 Received: from vegas.ks.uiuc.edu (vegas.ks.uiuc.edu [130.126.120.58]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g6HEaU809443; Wed, 17 Jul 2002 09:36:31 -0500 (CDT) Received: (from brunner@localhost) by vegas.ks.uiuc.edu (8.9.3+Sun/8.9.1) id JAA05984; Wed, 17 Jul 2002 09:36:30 -0500 (CDT) Date: Wed, 17 Jul 2002 09:36:30 -0500 From: Robert Brunner To: chemistry@ccl.net Subject: JMV Molecular Viewer Support within BioCoRE Message-ID: <20020717093630.A5976@ks.uiuc.edu> Reply-To: rbrunner@uiuc.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.3.19i JMV Molecular Viewer Support within BioCoRE July 3, 2002: Urbana, Illinois - The Theoretical Biophysics Group at the University of Illinois is proud to announce an exciting new feature of BioCoRE, a Biological Collaborative Research Environment. BioCoRE is freely accessible at the Theoretical Biophysics Group website and development is supported by the NIH National Center for Research Resources. JMV version 1.0 can now be accessed from within BioCoRE. JMV, a molecular viewer written using Java and Java 3D, can be used to view molecular files stored within the BioFS, BioCoRE's shared filesystem. JMV provides several molecular representations, multiple coloring styles, lighting controls, and stereoscopic rendering capabilities. Version 1.0 of JMV is currently only available within BioCoRE, and a standalone release is upcoming. In addition, several other BioCoRE components have seen key improvements recently: * The BioCoRE Control Panel can now be run as a standalone Java application using Java Web Start. This frees users from the constraints of running the Control Panel as a Java applet, which allows increased flexibility and improved robustness since browser crashes no longer kill the Control Panel. * Improved overall "look and feel". The BioCoRE web pages no longer rely on Javascript menus. This makes pages load faster and provides compatibility with more browsers. * Users can save JPEG files of states from VMD into BioCoRE automatically. This allows researchers to browse states visually and load desired configurations directly into VMD. * You can now create Interactive accounts within Job Management. Interactive accounts allow BioCoRE to submit jobs to any computer that you can log into via SSH. This can be used to run jobs on machines that BioCoRE doesn't officially support yet. (BioCoRE has built in support for machines at PSC, NCSA and Globus sites using the Alliance certificates) * BioCoRE job management can now upload files to the remote supercomputer center of your choice before submitting a job. This allows researchers to keep their input files in the BioCoRE shared filesystem and let BioCoRE automatically stage the files. For details, please visit the BioCoRE website at . The Theoretical Biophysics group encourages BioCoRE users to be closely involved in the development process through reporting bugs, contributing fixes, periodical surveys and via other means. Questions or comments may be directed to biocore@ks.uiuc.edu. We are eager to hear from you, and thank you for using our software! From chemistry-request@server.ccl.net Wed Jul 17 11:47:24 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g6HFlOw26063 for chemistry@ccl.net; Wed, 17 Jul 2002 11:47:24 -0400 Received: from KC-MAIL2.kc.umkc.edu ([134.193.143.162] RDNS failed) by kc-msxproto4.kc.umkc.edu with Microsoft SMTPSVC(5.0.2195.4905); Wed, 17 Jul 2002 09:54:27 -0500 content-class: urn:content-classes:message Subject: G98 B3LYP frequency Date: Wed, 17 Jul 2002 09:54:27 -0500 Message-ID: From: "Yang, Shizhong" To: Dear CCLers: I had got two optimized Gaussian98 output files about B3LYP nitrogen and silver cluster molecules. But when I try to find the frequency, I got 8 imaginary frequencies. Did I get the saddle points of the nitrogen and the cluster? What should I try next? By the way I donot know why the supercomputer's cpu usuage is 97% while memory is only 1.4% at most. Thank you in advance. Shizhong Yang sy2b2@umkc.edu Physics Department University of Missouri-Kansas City From chemistry-request@server.ccl.net Wed Jul 17 12:46:44 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HGkhv27567 for ; Wed, 17 Jul 2002 12:46:44 -0400 Received: from onco_irmb.health.nb.ca ([10.10.100.12]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-57574U3000L300S0V35) with ESMTP id ca for ; Wed, 17 Jul 2002 13:46:37 -0300 Message-Id: <5.1.1.6.0.20020717134221.009f62e0@mailhub.health.nb.ca> X-Sender: miroslavac@mailhub.health.nb.ca X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 17 Jul 2002 13:46:35 -0300 To: CCL From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) Subject: isoelectric point Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Dear All, I am looking for (ideally free) software that can calculate local isoelectric point (pI) for amino acids in a relatively large protein (~40kDa). Also I would appreciate information about references dealing with calculation of reactivity of cysteine residues in proteins. Thanks a lot for on-going help, Sincerely Mira Miroslava Cuperlovic-Culf Research Scientist Beausejour Medical Research Institute 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 e-mail: miroslavac@health.nb.ca From chemistry-request@server.ccl.net Wed Jul 17 13:43:20 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HHhKv28741 for ; Wed, 17 Jul 2002 13:43:20 -0400 Received: from eden.rutgers.edu (er4.rutgers.edu [165.230.180.142]) by goshen.rutgers.edu (Postfix) with ESMTP id 08388203ED; Wed, 17 Jul 2002 13:43:20 -0400 (EDT) Received: by eden.rutgers.edu (Postfix, from userid 37805) id 41DC915ECC; Wed, 17 Jul 2002 13:43:16 -0400 (EDT) Date: Wed, 17 Jul 2002 13:43:16 -0400 (EDT) From: Jianquan Chen X-Sender: jianquan@er4.rutgers.edu To: Carsten Detering Cc: chemistry@ccl.net Subject: Re: CCL:Gasteiger charges and Babel In-Reply-To: <000701c22872$79218d60$74805f80@donald> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII add -charge switch to babel command line. Good luck. jianquan chen Rutgers Univ. On Thu, 11 Jul 2002, Carsten Detering wrote: > Dear CCLers, > > I wonder how it is possible to assign Gasteiger charges to structures with > Babel. I looked on the web site and in the manual, but couldn't find a hint. > Would someone be so kind and point out to me how that works?? > Thanks a lot in advance, > > Carsten > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Wed Jul 17 15:47:20 2002 Received: from sprite.niddk.nih.gov ([128.231.4.189]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HJlKv31320 for ; Wed, 17 Jul 2002 15:47:20 -0400 Received: (from chanjcc@localhost) by sprite.niddk.nih.gov (8.8.8+Sun/8.8.8) id PAA00154; Wed, 17 Jul 2002 15:47:16 -0400 (EDT) Date: Wed, 17 Jul 2002 15:47:16 -0400 (EDT) From: "Chun Chung (Jerry) Chan" To: CHEMISTRY@ccl.net Subject: Sgi workstation for Quanta Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, we are considering to buy a new SGI workstation for running Quanta 97. Owing to the budget limit, we can only afford the starting configuration of the Fuel visual workstation (SGI VPro V10 graphics, 32MB of graphics memory, a 500MHz MIPS R14000A CPU with 2MB L2 cache, and 512MB memory). An alternative is to get an O2+ (32 bit) with the best possible configuration (MIPS@R12000A CPU with 2 MB L2 cache, 1 GB memory). My question is, does it really worth going for the Fuel visual station (e.g. I think a 50% gain in performance does not justify the Fuel)? I would be grateful to have your suggestions. Regards, Jerry ******************************************************************* * Jerry C. C. Chan phone: 301-402-4687 * * Laboratory of Chemical Physics fax: 301-496-0825 * * Room 406, Building 5, NIDDK http://samson3.uni-muenster.de * * National Institutes of Health * * Bethesda, MD20892, USA * ******************************************************************* From chemistry-request@server.ccl.net Wed Jul 17 13:12:05 2002 Received: from web13405.mail.yahoo.com ([216.136.175.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6HHC4v28002 for ; Wed, 17 Jul 2002 13:12:04 -0400 Message-ID: <20020717171204.48795.qmail@web13405.mail.yahoo.com> Received: from [128.115.13.33] by web13405.mail.yahoo.com via HTTP; Wed, 17 Jul 2002 10:12:04 PDT Date: Wed, 17 Jul 2002 10:12:04 -0700 (PDT) From: eric hu Subject: cartesian to pdb To: chemistry@ccl.net Cc: pdb-l@rcsb.org MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, I wonder if there is an easy way to change the cartesian coordinates to pdb format. Thanks! Eric __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com From chemistry-request@server.ccl.net Wed Jul 17 16:41:15 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HKfFv32032 for ; Wed, 17 Jul 2002 16:41:15 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id QAA12846; Wed, 17 Jul 2002 16:41:12 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3D35C920.15FD350@cornell.edu> Date: Wed, 17 Jul 2002 15:44:33 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: CHARMM HELP NEEDED!!! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I have what I think is a very strange problem. I'm curently using a "big" version of CHARMm, one that will handle 60,000+ atoms. I have built a system that consists of a glycosylated peptide having 27 amino acids and 21 mannoses. The system is solvated with 14,375 TIP3P waters, giving a total of 43,915 atoms. When I try and calculate the energy of the system with all the waters present, the energy goes through the roof; that is to say, I get stars instead of numbers for the energy. However, if I change the number of waters in the lines READ SEQUENCE TIP3 8844 GENERATE WAT NOANGLE NODIHE READ SEQUENCE TIP3 5531 GENERATE WAT2 NOANGLE NODIHE to this: READ SEQUENCE TIP3 5700 GENERATE WAT NOANGLE NODIHE CHARMm is able to read the structure in and calculate its energy. The other way, with 14,375 waters defined in the input file, it will read the structure in, but claculates the energy as *********. I don't want to go with only 5700 waters as my peptide won't be completely solvated. With the 14,375 waters, I have a shell around the peptide about 18 A thick. Obviously, I'm under the 60,000 atom limit, but I'm over some other limit that I'm not aware of. Has anyone encountered this problem before and how is it handled? Thank you in advance. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Jul 17 13:59:44 2002 Received: from dedalus.lcc.ufmg.br ([150.164.65.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HHxiv29162 for ; Wed, 17 Jul 2002 13:59:44 -0400 Received: from p333 (lcc-ip11.lcc.ufmg.br [150.164.65.210]) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id OAA24120 for ; Wed, 17 Jul 2002 14:59:28 -0300 Message-ID: <001701bd1665$d1d13a60$d241a496@p333> From: "=?iso-8859-1?Q?Andr=E9_M._de_Oliveira?=" To: Subject: CSSR containg charge information Date: Thu, 1 Jan 1998 01:31:50 -0200 Organization: UFOP MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0014_01BD1655.093D85A0" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0014_01BD1655.093D85A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers, Is anyone aware of any free PC-based conversion file able to = generate CSD CSSR files containing charge information (just like the = CSSR file from Tsar)? BABEL makes this conversion, but only with coordinates. I intend to = use this format in Somfa calculations. Regards. Andr=E9 Mauricio de Oliveira ------------------------------------------------------------------ N=FAcleo de Estudos em Qu=EDmica Medicinal Departamento de Qu=EDmica Universidade Federal de Minas Gerais VOICE: 55-31-499-5765 FAX: 55-31-499-5700 amolive@dedalus.lcc.ufmg.br www.qui.ufmg.br/~nequim ------=_NextPart_000_0014_01BD1655.093D85A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCLers,
 
    Is anyone aware of = any free=20 PC-based conversion file able to generate CSD CSSR files containing = charge=20 information (just like the CSSR file from Tsar)?
    BABEL makes this = conversion,=20 but only with coordinates. I intend to use this format in Somfa=20 calculations.
 
    = Regards.
 
Andr=E9 Mauricio de=20 Oliveira
-------------------------------------------------------------= -----
N=FAcleo=20 de Estudos em Qu=EDmica Medicinal
Departamento de = Qu=EDmica
Universidade=20 Federal de Minas Gerais
VOICE: 55-31-499-5765
FAX: = 55-31-499-5700
amolive@dedalus.lcc.ufmg.br
www.qui.ufmg.br/~nequim
------=_NextPart_000_0014_01BD1655.093D85A0-- From chemistry-request@server.ccl.net Sat Jul 13 12:15:39 2002 Received: from sintefxch1.sintef.no ([129.241.224.91]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6DGFcr00870 for ; Sat, 13 Jul 2002 12:15:39 -0400 Received: by sintefxch1.sintef.no with Internet Mail Service (5.5.2653.19) id <3WFD7V70>; Sat, 13 Jul 2002 18:15:36 +0200 Message-ID: <0832A8AC27425747B2873B96B7DF76EE6CF611@sintefxch1.sintef.no> From: Swang Ole To: "'chemistry@ccl.net'" Subject: Sorption isotherm simulation Date: Sat, 13 Jul 2002 18:15:35 +0200 Dear all, I need to perform simulations of isotherms for adsorption in crystalline microporous materials. Sorption energies are small; in the van der Waals range. So far, I have used an MC approach, as implemented in the SORPTION package sold by Accelrys. However, the software only is licensed for an old, slow workstation used by a number of people, severely limiting my possibilities. In the literature, most groups appear to use homebrew software for this kind of work. Some questions: What kind of software is available for this kind of calculations? Preferrably capable of grand canonical ensemble simulations. Two-body potentials will be sufficient. MC appears to be the favoured method for sorption calculations. Is simulated annealing a feasible alternative (I'd probably have to revert to non-grand canonical ensemble)? Any advice will be highly appreciated. I'll summarize if asked to do so. Thanks in advance, Ole Swang From chemistry-request@server.ccl.net Wed Jul 17 20:36:25 2002 Received: from melon.protagonist.com.au ([203.213.21.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6I0aNv13654 for ; Wed, 17 Jul 2002 20:36:24 -0400 Received: from mango.protagonist.com.au (mango.protagonist.com.au [172.17.2.4]) by melon.protagonist.com.au (8.12.1/8.12.1) with ESMTP id g6I0aHqL023828; Thu, 18 Jul 2002 10:36:17 +1000 Received: from mango.protagonist.com.au (localhost.localdomain [127.0.0.1]) by mango.protagonist.com.au (8.12.1/8.12.1) with ESMTP id g6I0aHmV020696; Thu, 18 Jul 2002 10:36:17 +1000 Received: from localhost (darwen@localhost) by mango.protagonist.com.au (8.12.1/8.12.1/Submit) with ESMTP id g6I0aHBT020693; Thu, 18 Jul 2002 10:36:17 +1000 Date: Thu, 18 Jul 2002 10:36:17 +1000 (EST) From: Paul Darwen To: chemistry@ccl.net Subject: Problem with Kabsch measure for RMSD on planar molecules Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I have a problem with the Kabsch method of measuring root-mean-square distance (RMSD) between molecules, as described in Kabsch 1978, Acta Cryst A34:827-828. As far as I can make out, the Kabsch method works so long as three or more planes are needed to intersect all the atoms. This means that if a molecule happens to (say) be in a single flat plane, then the Kabsch method chokes. For example, consider a molecule that's two carbon rings joined by a bridge. This makes it flat. Below are two Sybyl2 copies of this molecule, but rotated and translated. Their root-mean-square distance (RMSD) after alignment should be zero. But running Tinker's "superpose" program will align them lengthwise, but they're still rotated about the lengthwise axis and not aligned. The same thing happens in VMD if you try to align them with the script /usr/local/lib/vmd/scripts/vmd/rmsd.tcl Both of these incorrectly return an RMSD that's way more than zero. Has anyone written an RMSD measure that copes with planar molecules like this? If you can run the following two molecules through your align-and-measure-RMSD routine and get zero for an answer, I'd be grateful for a copy. __________________________________________________________________ Paul Darwen www.protagonist.com.au/darwen Protagonist Pty Ltd darwen@protagonist.com.au Brisbane 4064 Australia Phone: +61-7-3377-0304 --------------- This is the first of two molecules --------------- @MOLECULE Bridge bond between two carbon rings 22 23 1 SMALL NO_CHARGES @ATOM 1 C1 1.304260 1.349055 -0.389125 C.2 2 C2 1.980455 0.216229 -0.145061 C.2 3 C3 1.892984 -0.380446 1.046579 C.2 4 C4 1.123138 0.166682 1.990862 C.2 5 C5 0.447667 1.299539 1.744975 C.2 6 C6 0.512887 1.932896 0.546310 C.2 7 H7 -0.161845 1.681260 2.577240 H 8 H8 1.043615 -0.318373 2.979753 H 9 H9 2.448954 -1.312367 1.248134 H 10 H10 2.614125 -0.227590 -0.933089 H 11 H11 1.432842 1.773440 -1.395729 H 12 C12 -0.113409 3.725645 -0.903027 C.2 13 C13 -0.788738 4.858585 -1.148921 C.2 14 C14 -1.558584 5.405739 -0.204656 C.2 15 C15 -1.646220 4.808998 0.986939 C.2 16 C16 -0.970147 3.676100 1.230993 C.2 17 C17 -0.178748 3.092243 0.295605 C.2 18 H18 -1.098820 3.251664 2.237563 H 19 H19 -2.279900 5.252856 1.774946 H 20 H20 -2.114383 6.337763 -0.406164 H 21 H21 -0.709092 5.343685 -2.137780 H 22 H22 0.496097 3.343872 -1.735268 H @BOND 1 1 2 1 2 1 6 1 3 1 11 1 4 2 3 1 5 2 10 1 6 3 4 1 7 3 9 1 8 4 5 1 9 4 8 1 10 5 6 1 11 5 7 1 12 6 17 1 13 12 13 1 14 12 17 1 15 12 22 1 16 13 14 1 17 13 21 1 18 14 15 1 19 14 20 1 20 15 16 1 21 15 19 1 22 16 17 1 23 16 18 1 @SUBSTRUCTURE 1 **** 1 --------------- This is the second of two molecules --------------- @MOLECULE Bridge bond between two carbon rings 22 23 1 SMALL NO_CHARGES @ATOM 1 C1 0.054840 0.525138 -1.730657 C.2 2 C2 1.112013 -0.267815 -1.962393 C.2 3 C3 2.327386 0.082664 -1.533765 C.2 4 C4 2.474774 1.233137 -0.871667 C.2 5 C5 1.416448 2.024847 -0.640943 C.2 6 C6 0.167392 1.700650 -1.061558 C.2 7 H7 1.626775 2.952893 -0.089236 H 8 H8 3.475262 1.532683 -0.512794 H 9 H9 3.197548 -0.569107 -1.724045 H 10 H10 0.978844 -1.216950 -2.510944 H 11 H11 -0.908118 0.160964 -2.117910 H 12 C12 -0.802543 3.687019 -0.155836 C.2 13 C13 -1.859722 4.479966 0.075891 C.2 14 C14 -3.075096 4.129477 -0.352705 C.2 15 C15 -3.222482 2.979014 -1.014814 C.2 16 C16 -2.164151 2.187340 -1.245587 C.2 17 C17 -0.915090 2.511520 -0.824932 C.2 18 H18 -2.374444 1.259272 -1.797273 H 19 H19 -4.223035 2.679500 -1.373569 H 20 H20 -3.945250 4.781258 -0.162414 H 21 H21 -1.726500 5.429133 0.624380 H 22 H22 0.160424 4.051217 0.231410 H @BOND 1 1 2 1 2 1 6 1 3 1 11 1 4 2 3 1 5 2 10 1 6 3 4 1 7 3 9 1 8 4 5 1 9 4 8 1 10 5 6 1 11 5 7 1 12 6 17 1 13 12 13 1 14 12 17 1 15 12 22 1 16 13 14 1 17 13 21 1 18 14 15 1 19 14 20 1 20 15 16 1 21 15 19 1 22 16 17 1 23 16 18 1 @SUBSTRUCTURE 1 **** 1 --------------- End of the second of two molecules --------------- From chemistry-request@server.ccl.net Wed Jul 17 19:19:16 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6HNJGv06664 for ; Wed, 17 Jul 2002 19:19:16 -0400 Received: from HSC-DOM5-MTA by GWIA.HSC.WVU.EDU with Novell_GroupWise; Wed, 17 Jul 2002 19:19:10 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.2 Beta Date: Wed, 17 Jul 2002 19:18:42 -0400 From: "Peter Gannett" To: , Cc: Subject: Re: CCL:cartesian to pdb Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Eric: While I'm not exactly sure what your cartesian coordinate file looks like, you might try babel http://smog.com/chem/babel/ Pete >>> eric hu 07/17/02 01:12PM >>> Hi, I wonder if there is an easy way to change the cartesian coordinates to pdb format. Thanks! Eric __________________________________________________ Do You Yahoo!? Yahoo! Autos - Get free new car price quotes http://autos.yahoo.com -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net