From chemistry-request@www.ccl.net Mon Oct 19 07:45:42 1998 Received: from naveen.ncst.ernet.in (naveen.ncst.ernet.in [202.41.110.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA07679 Mon, 19 Oct 1998 07:45:28 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.9.1/8.9.1) with SMTP id RAA08074 for ; Mon, 19 Oct 1998 17:17:59 +0530 (GMT+05:30) Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA15641; Mon, 19 Oct 1998 17:11:15 +0500 Received: by (5.x/SMI-SVR4) id AA17409; Mon, 19 Oct 1998 16:44:30 -0500 Date: Tue, 20 Oct 1998 02:44:29 +0500 (GMT-5) From: Sangeeta Sawant To: Computational Chemistry List Subject: Wanted program for superimposing peptides/proteins Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! I would like to know if there is any software/program (preferably shareware/public-domain) which allows to superimpose several protein/peptide conformations onto one (say, template confo.) in a batch mode. The program may be for either IRIX or OS2 (DEC-ALPHA) or SOLARIS or LINUX or DOS (No Mac-OS please). Any help will be appreciated. Thanks in advance. Sangeeta +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mrs. Sangeeta Sawant + + Research Fellow email : sangeeta@bioinfo.ernet.in + + Bioinformatics Centre phone : +91-212-355039 + + University of Pune fax : +91-212-350087 + + Ganeshkhind + + Pune - 411007 + + India. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Mon Oct 19 08:45:02 1998 Received: from naveen.ncst.ernet.in (naveen.ncst.ernet.in [202.41.110.35]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA16955 Mon, 19 Oct 1998 08:44:51 -0400 (EDT) Received: from iucaa (iucaa.ernet.in [202.141.155.1]) by naveen.ncst.ernet.in (8.9.1/8.9.1) with SMTP id SAA11918 for ; Mon, 19 Oct 1998 18:17:55 +0530 (GMT+05:30) Received: from iucaa by iucaa (5.65v3.2/SMI-4.1) id AA23964; Mon, 19 Oct 1998 18:11:13 +0500 Received: by (5.x/SMI-SVR4) id AA17500; Mon, 19 Oct 1998 17:56:22 -0500 Date: Tue, 20 Oct 1998 03:56:21 +0500 (GMT-5) From: Sangeeta Sawant To: Computational Chemistry List Subject: Blast with PDBSelect (fwd) Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I would like to know if there is any server where I can run the Blastp program (any version, gapped or ungapped will do) in which the database option is the set of proteins defined by Hobohm et.al. known as "PDBSELECT". (This set of proteins lists the proteins from PDB, having different percent sequence similarities.) TIA for the replies. I'll summarize. Sangeeta +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Mrs. Sangeeta Sawant + + Research Fellow email : sangeeta@bioinfo.ernet.in + + Bioinformatics Centre phone : +91-212-355039 + + University of Pune fax : +91-212-350087 + + Ganeshkhind + + Pune - 411007 + + India. + +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@www.ccl.net Mon Oct 19 15:29:25 1998 Received: from mx1.cso.uiuc.edu (mx1.cso.uiuc.edu [128.174.5.37]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA27202 Mon, 19 Oct 1998 15:29:24 -0400 (EDT) Received: from london.ks.uiuc.edu (london.ks.uiuc.edu [128.174.214.2]) by mx1.cso.uiuc.edu (8.8.8/8.8.8) with ESMTP id OAA20567 for ; Mon, 19 Oct 1998 14:28:54 -0500 (CDT) Received: from ks.uiuc.edu (jerusalem.ks.uiuc.edu) by london.ks.uiuc.edu with ESMTP (1.37.109.20/16.2) id AA191905331; Mon, 19 Oct 1998 14:28:51 -0500 Sender: ferenc@ks.uiuc.edu Message-Id: <362B92F1.2CBBC947@ks.uiuc.edu> Date: Mon, 19 Oct 1998 14:28:49 -0500 From: Ferenc Molnar Organization: TB group, Beckman Inst., UIUC X-Mailer: Mozilla 4.03 [en] (X11; I; IRIX 5.3 IP22) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: gold surface parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all: I would appreciate very much pointers to procedures for parametrizing the interaction of organic molecules with gold-surfaces (not parametrization in general!). Has anybody done MD or MC simulations on these or similar systems? A preliminary literature search did not result in too many useful references ... Thank you very much for your time! -Ferenc From chemistry-request@www.ccl.net Mon Oct 19 18:16:01 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA25539 Mon, 19 Oct 1998 18:16:00 -0400 (EDT) Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) with SMTP id RAA33956 for ; Mon, 19 Oct 1998 17:19:54 -0500 (CDT) Date: Mon, 19 Oct 1998 17:19:54 -0500 (CDT) From: Tapas Kar To: "Comp. Chem. List" Subject: Density difference plot Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Looking for software/program (preferably shareware/public-domain) which reads Gaussian output/checkpoint files and draw density/density difference plots. The program may be for either IBM/rs6000 or Window98/NT. Tapas ------------------------------------------- Tapas Kar, Ph. D Asst. Scientist/Asst. Professor (Adjunct) Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) -------------------------------------------- From chemistry-request@www.ccl.net Mon Oct 19 18:22:11 1998 Received: from guarneri.curagen.com (guarneri.curagen.com [199.183.38.51]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA26433; Mon, 19 Oct 1998 18:22:10 -0400 (EDT) Received: from curagen.com (pc27.curagen.com [172.16.4.127]) by guarneri.curagen.com (8.8.8/8.8.8) with ESMTP id SAA01970; Mon, 19 Oct 1998 18:18:54 -0400 (EDT) Message-ID: <362BC81B.4B04D8DD@curagen.com> Date: Mon, 19 Oct 1998 19:15:39 -0400 From: Andreas Windemuth Organization: Curagen Corporation X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: Iraj Daizadeh CC: chemistry@www.ccl.net, chemistry-request@www.ccl.net, mleach@curagen.com Subject: Re: CCL:BioInformatics. References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You may want to try CuraTools, our sequence analysis package which is freely available for use on the World Wide Web. Visit "http://www.curagen.com" and choose "CuraTools". Andreas Windemuth CuraGen Corporation 555 Long Wharf Drive New Haven, CT 06511 Iraj Daizadeh wrote: > > Hello. > > I am interested in obtaining codes (written in any language) that are free > or relatively free (< $500.00) for members in academia that can visualize > and manipulate Genetic Database Information (nucleic acid sequences, > etc...) for problems in BioInformatics. I will summarize all respones as > is traditional on the CCL. > > Sincerely, > > Iraj. > > Iraj Daizadeh, Ph.D. > Harvard University > Department of Chemistry and Chemical Biology > 12 Oxford Street, Box #35 > Cambridge, MA 02138-2902 > Phone: 617-495-2654 > Fax: 617-495-1823 > email: daizadeh@lhasa.harvard.edu > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- From chemistry-request@www.ccl.net Mon Oct 19 21:36:39 1998 Received: from risky3.thchem.siu.edu (risky3.thchem.siu.edu [131.230.89.13]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA28396 Mon, 19 Oct 1998 21:36:38 -0400 (EDT) Received: from localhost (tapas@localhost) by risky3.thchem.siu.edu (AIX4.2/UCB 8.7/8.7) with SMTP id UAA33066 for ; Mon, 19 Oct 1998 20:40:33 -0500 (CDT) Date: Mon, 19 Oct 1998 20:40:33 -0500 (CDT) From: Tapas Kar To: "Comp. Chem. List" Subject: Summary: CPU-MEM-RWF relation from G94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > To check the effect of %MEM on G94 jobs, i did 4 CCSD(T) freq > calculations using same input file but different %MEM=32, 64, 128 and > 150MB. No other application prog. was running during these four jobs. > > The result is: > %MEM CPU RWF(MB) MaxMem (from output) > 32mb 55m 35.2s 45 4194304 > 64mb 57m 11.8s 77 8388608 > 128mb 59m 37.5s 141 16777216 > 150mb 1h 0m 25.5s 163 19660800 > > It looks odd. Expert's comment please. > Tapas > PS: I am using RS/6000 Model 590 and AIX4.2 > Total 256mb memory and 13(2+2+9)gb hard disk. > **************************************************************************** AIX uses the spare RAM memory as the disk cache. Thus when you allocate memory to G94 with the %MEM directive you are also actually reducing the disk cache, slowing iour I/O. If your job is disk-intensive ( like CC ) it is reasonably possible to observe behaviors like the one you experience just my 0.02$ Ivan -- Dr. Ivan Rossi - Computational Chemistry Consultant e-mail: ivan@lipid.biocomp.unibo.it phone: (+39)-051-456177 ****************************************************************************** Though not an expert, I may have some relevant observations to share. You point out something odd about the Gaussian programs, namely the less-than-intuitive relationship between the amount of memory allocated and the ressources used. We have recently run a series of tests on a variety of machines to examine these relationships, but I'm afraid that in the end we were only confused, abeit on a higher level. We concentrated our efforts on time-consuming jobs, which in our line of work means MP2/4 and QCISD(T) calculations (G2 and CBS-Q methods). The results are somewhat dependent upon the size of the system and upon the hardware employed. For a relatively small open-shell system (a C3H7N radical cation) we found that the UMP2/6-311+G(3df,2p) step of a G2(MP2) calculation on a single node of an IBM SP2 cluster would use within reason the same amount of cpu time, regardless of whether the job was allowed to use (%Mem) 4MW, 16MW, or 64MW of memory. The reported maximum size of the read-write file in the three runs was 700MB, 365MB, and 633MB; in two runs using 10MW and 100MW we observed that the read-write file was almost three times bigger in the 100MW run than in the 10MW run (900MB vs 350MB). The QCISD(T)/6-311G(d,p) step ran 30% faster when 64MW were available (for the C3H7N+. system, the memory required for AO integral storage is 25MW); the time used for the triples was the same, regardless of the %Mem setting. (see below). Doing CBS-Q calculations on an SGI Origin200 for a C3H7O cation, we found that the execution times would vary only little with the amount of memory allocated (8MW, 16MW, 32MW, 48MW). The memory required for in-memory allocated (1.33GB, 1.39GB, 1.51GB, 1.64GB). QCISD(T)/6-31G(d) calculations (Origin200) for a somewhat bigger system (a C4H12N cation) indicated that the QCISD step would benefit from increased memory (test runs with 8MW, 16MW, 32MW, 48MW; in-memory storage of AO integrals requiring 25MW), but that, strangely enough, the triples calculations would actually slow down. To examine this further we did QCISD(T)/6-31G(d) calculations for C5H14N cations on an SGI Origin200, on a single node of an IBM SP2 cluster, and on a Fujitsu VX1. In all three instances we observed that the cpu-time for the triples calculations would INCREASE quite a bit with increased memory (data points: SGI 246 min (10MW), 321 min (60MW); IBM 97 min (16MW), 209 min (80MW); the memory required for AO integral storage was 51MW; similar results on the Fujitsu machine). These slow-downs were on all three machines to some extent off-set by a more rapid execution of the QCISD step with increased memory. Also here we observed that increased memory would be accompanied by an increase in the size of the read-write file. Since doing these calculations I have been told that also other people have observed that the cpu-time used by the Gaussian programs for highly correlated calculations can show an inverse dependence on the amount of memory allocated. I don't know if these things have changed in Gaussian98. Hope this helps. Steen -- Steen Hammerum steen@kiku.dk Department of Chemistry (+45) 35 32 02 08 University of Copenhagen, Denmark fax: (+45) 35 32 02 12 **************************************************************************** -------------------------------------------- Tapas Kar, Ph. D Asst. Scientist/Asst. Professor (Adjunct) Forestry Bldg 118 Department of Chemistry Southern Illinois University at Carbondale Illinois 62901-4409 Fax: (618) 453 6408 Tel: (618) 453 6433(Lab) 6485(Office) --------------------------------------------