From owner-chemistry@ccl.net Sun Oct 21 00:30:01 2007 From: "Jinsong Zhao jszhao(-)mail.hzau.edu.cn" To: CCL Subject: CCL: Input file for STERIMOL program Message-Id: <-35432-071021002822-21372-OuMcYGARiJ2Q5zBbaq6h5w ~ server.ccl.net> X-Original-From: "Jinsong Zhao" Date: Sun, 21 Oct 2007 00:28:08 -0400 Sent to CCL by: "Jinsong Zhao" [jszhao^_^mail.hzau.edu.cn] > Sent to CCL by: "Tamas Gunda" [tgunda1++puma.unideb.hu] > I have the documentation somewhere, but I need time to find it... > However, try to use the program Mol2mol to calculate the sterimol > parameters. It uses the original algorythm and accepts a lot of > common input formats. > http://web.interware.hu/frenzy/mol2mol/ > Tamas Gunda > = = = = = = = = = = = = > Prof. Tamas E. Gunda > University of Debrecen > Department of Pharmaceutical Chemistry > H-4010 Debrecen, POB 36, Hungary > tgunda2 {at} puma.unideb.hu Dear Prof. Gunda, Thank you very much for your reply to my post on CCL list. I will appreciate if you could find the documentation and send a copy to me. I will try program Mol2mol, however, I also hope I could get some information on the input file for original program STERIMOL. Thanks again! Best regards, Jinsong -- Jinsong Zhao, Dr. College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, P. R. China E-mail: jszhao::mail.hzau.edu.cn From owner-chemistry@ccl.net Sun Oct 21 01:07:01 2007 From: "Jinsong Zhao jszhao###mail.hzau.edu.cn" To: CCL Subject: CCL: Input file for STERIMOL program Message-Id: <-35433-071021003502-23452-tlvfyTwp/KULOfHT0EValw ~ server.ccl.net> X-Original-From: "Jinsong Zhao" Date: Sun, 21 Oct 2007 00:34:58 -0400 Sent to CCL by: "Jinsong Zhao" [jszhao * mail.hzau.edu.cn] > Sent to CCL by: Steve Bowlus [chezbowlus^comcast.net] > I have some additional, more detailed information on STERIMOL which > I believe did not make it into the QCPE documentation packet (I don't > remember what is in the deposited version). Please give me a few days > to dig through my files to locate this information. > > Can anyone suggest an additional repository for this information? > Stuff keeps disappearing out of my personal archives ... > > Cheers, > Steve Bowlus > (ported Sterimol to the PC) > Thank you very much for your reply to my post on CCL. If you happen to find some additional information on STERIMOL, would you like to send a copy to this mail box? Thanks in advance! Best regards, Jinsong -- Jinsong Zhao, Dr. College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, P. R. China E-mail: jszhao!^!mail.hzau.edu.cn From owner-chemistry@ccl.net Sun Oct 21 10:44:01 2007 From: "Jozsef Csontos jozsefcsontos~!~creighton.edu" To: CCL Subject: CCL: Parallel runs in Turbomole Message-Id: <-35434-071021104130-7580-SDvZVsytDiydtjwew10+SA-.-server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sun, 21 Oct 2007 09:41:16 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos^_^creighton.edu] Hi, I have no experience with turbomole at all but it seems to me that you don't have passwordless connection to the working nodes. (You said "when I launch the executable (e.g. jobex -ri) the calculation crashes after entering my ssh password") You should work on this issue. (for example: generate a public key with "ssh-keygen -t rsa" on the master node then put the content of the generated file into the authorized_keys file on the working nodes "cat ~/.ssh/id_rsa.pub | ssh hostname_of_your_working_node "cat- >> ~/.ssh/authorized_keys") However, this procedure strongly depends on your cluster configuration. I hope it helps, Jozsef On Fri, 2007-10-19 at 22:27 -0400, Gonzalo Jim nez-Os s gjimenez,,unizar.es wrote: > Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez[-]unizar.es] > Dear CCL'ers > > In the last days I've doing some benchmarking with Turbomole, and I am experiencing some kind of trouble when submitting parallel jobs. Whereas the serial jobs run in a really straightforward and quick fashion, every parallel run crashes at its first calculation stages. I do believe that I have set up the parallel environment correctly by following the manual guidelines: > > export PARA_ARCH=MPI > export PATH=TURBODIR/bin/sysname:PATH > export PARNODES=2 > > My sysname seems to be OK (em64t-unknown-linux-gnu_mpi), but when I launch the executable (e.g. jobex -ri) the calculation crashes after entering my ssh password. Here is the output: > > ***************************** > convgrep will be taken out of the TURBODIR directory > Password: > /opt/soft/tmoleX/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/ridft_mpi: error while loading shared libraries: libguide.so: cannot open shared object file: No such file or directory > /opt/soft/tmoleX/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/ridft_mpi: error while loading shared libraries: libguide.so: cannot open shared object file: No such file or directory > MPI Application rank 0 exited before MPI_Init() with status 127 > OPTIMIZATION CYCLE 1 > Password: > /opt/soft/tmoleX/TURBOMOLE/bin/em64t-unknown-linux-gnu_mpi/rdgrad_mpi: error while loading shared libraries: libguide.so: cannot open shared object file: No such file or directory > MPI Application rank 0 exited before MPI_Init() with status 127 > relax ended abnormally > program stopped. > relax ended abnormally > program stopped. > run relax for a cartesian step > relax ended abnormally > program stopped. > ERROR: Module relax failed to run properly - please check output job.1 and job.last for the reason > ***************************** > > It seems like it does not find de shared libraries that I have located in TURBODIR/libso/em64t-unknown-linux-gnu_mpi. It is a bit confusing to me... > Any idea about that? I am currently using Intel EM64T Dual Core processors. > > On the other hand, do you know about any benchmark results centered on the scaling ability of Turbomole? > > Regards, > > Gonzalo> > > -- Jozsef Csontos, Ph.D. (jozsefcsontos_at_creighton.edu) Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Sun Oct 21 14:21:01 2007 From: "David Hose anthrax_brothers,+,hotmail.com" To: CCL Subject: CCL: Wavelet Analysis of Molecular Surface Properties. Message-Id: <-35435-071021141955-14658-T+6LV9hCwxrF9Va1bP/2Yw%%server.ccl.net> X-Original-From: "David Hose" Date: Sun, 21 Oct 2007 14:19:51 -0400 Sent to CCL by: "David Hose" [anthrax_brothers%hotmail.com] Hi Guys, Ive got a problem that you might be able to help me with, or at least point me in the right direction. Heres some background. As you all know, molecular surfaces are useful in explaining certain molecular phenomena. What I want to do, is take these 4D surfaces and compress them as a 2D graph, by dividing the surface up into tesserae, and then plotting a charge/frequency chart from them. This approach has been used by Liu at Virginia Tech to create sigma profiles using COSMO surfaces (http://www.design.che.vt.edu/VT-2005.html). If I recall correctly, regular contributor to this list, Andreas Klamt has also done something related to this as well. I came across a PowerPoint presentation some months ago that mentioned that these types property/ frequency charts can be compressed by using Wavelet analysis. Unfortunately, I cant find the presentation again. So my question is, how can I compress these property/frequency charts using Wavelet Analysis? If anyone can point me in the right direction of the maths / algorithms I would grateful. TIA. Dave. From owner-chemistry@ccl.net Sun Oct 21 15:42:01 2007 From: "Curt M. Breneman brenec**rpi.edu" To: CCL Subject: CCL: Wavelet Analysis of Molecular Surface Properties. Message-Id: <-35436-071021154123-22672-rW+QlYck/HbnMt09QKmgFg!A!server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Sun, 21 Oct 2007 15:40:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec ~ rpi.edu] Dear Dave, You may have seen a presentation from my group concerning the use of wavelet coefficients for encoding molecular surface properties. Our recent chapter in Reviews in Computational Chemistry entitled "Wavelets in Chemistry" also describes this work. The ability to perform discrete wavelet transformation analysis of molecular surface property distributions is part of our program suite called "PEST" - or Property-Encoded Surface Translator, which also produces a number of other surface-based descriptors, including surface property histograms, surface autocorrelation analysis and our version of ray-tracing shape/property descriptors (of which Zahuar's "Shape Signatures" is another example). Please see the RECCR website for additional details, or contact me directly for further information. http://reccr.chem.rpi.edu Cheers, Curt Breneman RPI Chemistry Director, RECCR Cheminformatics Center ==============Original message text=============== On Sun, 21 Oct 2007 14:19:51 EDT "David Hose anthrax_brothers,+,hotmail.com" wrote: Sent to CCL by: "David Hose" [anthrax_brothers%hotmail.com] Hi Guys, Ive got a problem that you might be able to help me with, or at least point me in the right direction. Heres some background. As you all know, molecular surfaces are useful in explaining certain molecular phenomena. What I want to do, is take these 4D surfaces and compress them as a 2D graph, by dividing the surface up into tesserae, and then plotting a charge/frequency chart from them. This approach has been used by Liu at Virginia Tech to create sigma profiles using COSMO surfaces (http://www.design.che.vt.edu/VT-2005.html). If I recall correctly, regular contributor to this list, Andreas Klamt has also done something related to this as well. I came across a PowerPoint presentation some months ago that mentioned that these types property/ frequency charts can be compressed by using Wavelet analysis. Unfortunately, I cant find the presentation again. So my question is, how can I compress these property/frequency charts using Wavelet Analysis? If anyone can point me in the right direction of the maths / algorithms I would grateful. TIA. Dave.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text===========