From owner-chemistry@ccl.net Thu Dec 22 15:50:00 2005 From: "Denys Bashtovyy bashtovyy*_*go.com" To: CCL Subject: CCL: "salt bridges" vs "hydrogen bonds" in protein structures Message-Id: <-30384-051222153938-25271-Zic/xRvRePuQ/9d2H0ezFA*_*server.ccl.net> X-Original-From: "Denys Bashtovyy" Sent to CCL by: "Denys Bashtovyy" [bashtovyy(!)go.com] Dear All, Are there any known salt bridges in resolved protein structures, or those "salt bridges" are just misnamed hydrogen bonds? Can a protein "salt bridge" have a partially positive hydrogen atom as its part? thanks, Denys From owner-chemistry@ccl.net Thu Dec 22 16:25:01 2005 From: "Ivanciuc, Ovidiu I. oiivanci(!)utmb.edu" To: CCL Subject: CCL: Is there any book/review/web to learn QSAR/QSAR-3D from the basis? Message-Id: <-30385-051222155319-28117-mRUrwddZPKD1zs/G7shebA##server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 22 Dec 2005 14:18:29 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci-x-utmb.edu] >>>Please let me know the free web based information >>> for above papers Free papers on QSAR can be found in the IEJMD journal, http://www.biochempress.com Go to PubMed to search for other QSAR papers (some are free): http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed Regards, Ovidiu Ivanciuc ********************************* Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Biochemistry and Molecular Biology University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA From owner-chemistry@ccl.net Thu Dec 22 17:00:00 2005 From: "Ivanciuc, Ovidiu I. oiivanci{:}utmb.edu" To: CCL Subject: CCL: what r the steps in the creation of a software 4 toxicity prediction of ligands Message-Id: <-30386-051222155321-28162-7CaH/yRsdgnKq6QnqStO9A]![server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="Windows-1252" Date: Thu, 22 Dec 2005 14:15:32 -0600 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci/./utmb.edu] >>pl help by telling how 2 proceed in the project(toxicity prediction) The first step would be to read papers on toxicity prediction. PubMed, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed, is a good starting point. Related papers can be found in molecular modeling journals, such as IEJMD (http://www.biochempress.com). >>can i use neural networks or alternative mapping methods >> like recursive partitioning or SVM. You can use all these methods, and any other QSAR technique. Nobody can tell which method gives the best prediction for a particular dataset. However, for specific biological activities (e.g., mutagenicity, carcinogenicity) there are dedicated systems that consider information regarding the receptor, metabolism, mechanism, etc. Best regards, Ovidiu Ivanciuc ********************************* Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Biochemistry and Molecular Biology University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA From owner-chemistry@ccl.net Thu Dec 22 17:34:00 2005 From: "David F. Green dfgreen-.-ams.sunysb.edu" To: CCL Subject: CCL: "salt bridges" vs "hydrogen bonds" in protein structures Message-Id: <-30387-051222171747-26466-bpIXV2T4DnZqxEt+U50tGw ~~ server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 22 Dec 2005 17:17:24 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen[]ams.sunysb.edu] This is really just an issue of semantics. Salt bridge (or ion pair) is not an orthogonal term to hydrogen bond, it simply describes the interaction of a pair (or more) of groups with net charges. The interaction of these groups may involve hydrogen bonds, but due to the significant monopole, there is much more going on in the interaction than simply the hydrogen bonding. That said, you may loosely categorize salt-bridges into hydrogen bonding and non-hydrogen bonding, but both are observed. This is not an issue of resolution; in many cases the geometry imposed by the protein structure simply can not accomodate hydrogen bonding, and yet an electrostatic interaction is still made. Also, the distinction of whether the groups are hydrogen bonded or not is rather poorly defined; depending on what you consider the angular dependence of hydrogen bond formation to be, you will classify the interactions differently. For this reason, many people simply use the two classes of (1) salt-bridges (regardless of hydrogen bonding) and (2) polar (neutral) hydrogen bonds in discussing electrostatic interactions. All of this has been well discussed in the literature. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Denys Bashtovyy bashtovyy*_*go.com wrote: > Sent to CCL by: "Denys Bashtovyy" [bashtovyy(!)go.com] > Dear All, > > Are there any known salt bridges in resolved protein structures, or those "salt bridges" are just misnamed hydrogen bonds? > > Can a protein "salt bridge" have a partially positive hydrogen atom as its part? > > thanks, > > Denys> > > From owner-chemistry@ccl.net Thu Dec 22 20:28:00 2005 From: "JAMES VIVIAN jamestvivian*|*msn.com" To: CCL Subject: CCL: what r the steps in the creation of a software 4 toxicity prediction of Message-Id: <-30388-051222185255-10410-RCR2Uo1WWt+b0EJ/rSBF5Q],[server.ccl.net> X-Original-From: "JAMES VIVIAN" Content-Type: text/plain; format=flowed Date: Thu, 22 Dec 2005 18:05:41 -0500 Mime-Version: 1.0 Sent to CCL by: "JAMES VIVIAN" [jamestvivian^-^msn.com] I would strongly recommend that in the absence of other information, try using recursive partitioning as a first cut at the problem. Use simple 2-d descriptors and start with a single, "greedy" tree. Depending on how much response data is available, build a random forest of trees. And pay attention to the p-values. Good luck. ~Jim Vivian >From: "Ivanciuc, Ovidiu I. oiivanci{:}utmb.edu" >Reply-To: "CCL Subscribers" >To: "Vivian, James T " >Subject: CCL: what r the steps in the creation of a software 4 toxicity >prediction of ligands >Date: Thu, 22 Dec 2005 17:21:48 -0500 > >Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci/./utmb.edu] > > > >>pl help by telling how 2 proceed in the project(toxicity prediction) >The first step would be to read papers on toxicity prediction. >PubMed, http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed, >is a good starting point. >Related papers can be found in molecular modeling journals, >such as IEJMD (http://www.biochempress.com). > > >>can i use neural networks or alternative mapping methods > >> like recursive partitioning or SVM. >You can use all these methods, and any other QSAR technique. >Nobody can tell which method gives the best prediction for a >particular dataset. > >However, for specific biological activities (e.g., mutagenicity, >carcinogenicity) there are dedicated systems that consider >information regarding the receptor, metabolism, mechanism, etc. > >Best regards, >Ovidiu Ivanciuc >********************************* >Ovidiu Ivanciuc >Sealy Center for Structural Biology, >Department of Biochemistry and Molecular Biology >University of Texas Medical Branch, >301 University Boulevard, >Galveston, Texas 77555-0857 >USA> > > From owner-chemistry@ccl.net Thu Dec 22 23:22:00 2005 From: "Chung Lee s4553711*o*yahoo.com.tw" To: CCL Subject: CCL:G: Problem in running parallel G03 job Message-Id: <-30389-051222230632-29710-BbgGIWqRr2KLrAsDdmnSfQ : server.ccl.net> X-Original-From: "Chung Lee" Sent to CCL by: "Chung Lee" [s4553711|a|yahoo.com.tw] Dear CCLers, We have installed a small Linux cluster with OS of Fedora 3.0. The G03 job works pretty good on a single CPU. In addition, we are also able to run parallel CHARMM job. However, we have difficulty to run parallel G03L job via Linda 7.1. When the verbose option of Linda is turned on, we have the following error message as shown below. Any suggestion or advise is welcome! Thanks. Lee. error message at the end of output ================================== .... ..... Rotational constants (GHZ): 2.6971930 0.2674771 0.2434224 Standard basis: 6-31G(d,p) (6D, 7F) There are 270 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 270 basis functions, 476 primitive gaussians, 270 cartesian basis functions 48 alpha electrons 48 beta electrons nuclear repulsion energy 733.7849494285 Hartrees. NAtoms= 26 NActive= 26 NUniq= 26 SFac= 1.00D+00 NAtFMM= 60 Big=F Incorrectly built binary which accesses errno or h_errno directly. Needs to be fixed. ntsnet: using global map file "/pub/g03/linda7.1/intel-linux2.4/../common/lib/tsnet.map" ntsnet: using user map file "/home/user/.tsnet.map" ntsnet: checking for /pub/g03/linda-exe/l302.exel ntsnet: using executable file /pub/g03/linda-exe/l302.exel ntsnet: maxlicense is 1000000 ******************************************** appl config file: /pub/g03/linda-exe/tsnet.config-l302_exel user config file: /home/user/.tsnet.config global config file: /pub/g03/linda7.1/intel-linux2.4/../common/lib/tsnet.config user map file: /home/user/.tsnet.map global map file: /pub/g03/linda7.1/intel-linux2.4/../common/lib/tsnet.map local node: cluster1 remote nodes: node1 node2 nodelist: node1 node2 nodefile: tsnet.nodes minwait: 600 maxwait: 600 workerwait: 900 masterload: 1.000000 workerload: 1.000000 fallbackload: 0.990000 maxprocspernode: 1 delay: 0 maxnodes: Number of available nodes minworkers: 2 maxworkers: 2 loadperiod: 5 high: True suffix: True verbose: True veryverbose: True distribute: False cleanup: True getload: False translate: True useglobalconfig: True useglobalmap: True application name: l302.exel application lookup name: l302_exel local executable directory: /pub/g03/linda-exe distribution directory: /pub/g03/linda7.1/intel-linux2.4/ maxlicense: 1000000 ******************************************** ntsnet: trying to schedule 2 workers ntsnet: scheduled a total of 2 workers ******************************************** node name: cluster1 official node name: cluster1.private.net config lookup name: cluster1 executable directory: /pub/g03/linda-exe executable name: l302.exel working directory: /home/user/g03test debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: True processes scheduled: 1 (including master process) maximum processes: 1 ******************************************** node name: node1 official node name: node1.private.net config lookup name: node1 executable directory: /pub/g03/linda-exe executable name: l302.exel working directory: /home/user/g03test debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: False processes scheduled: 1 maximum processes: 1 ******************************************** node name: node2 official node name: node2.private.net config lookup name: node2 executable directory: /pub/g03/linda-exe executable name: l302.exel working directory: /home/user/g03test debugger: linda rsh argument: rsh linda rcp argument: user: adjusted load: 1.000000 threshold: 20.000000 speedfactor: 1.000000 available: True nice: False master: False processes scheduled: 1 maximum processes: 1 ******************************************** ntsnet: starting master process on cluster1.private.net /pub/g03/linda7.1/intel-linux2.4/bin/linda_sh /pub/g03/linda-exe/l302.exel 15728640 transstilbene.chk 1 /home/user/g03test/Gau-4924.int 0 /home/user/g03test/Gau-4924.rwf 0 /home/user/g03test/Gau-4924.d2e 0 /home/user/g03test/Gau-4924.scr 0 /home/user/g03test/Gau-4923.inp 0 junk.out 0 +LARGS 3 0 -kainterval 1 -master 9497 -tsnetport 35862 -maxworkers 2 -minworkers 2 -minwait 600 -maxwait 600 -nodename cluster1.private.net -kaon ntsnet: starting 1 worker on node1.private.net /pub/g03/linda7.1/intel-linux2.4/bin/linda_rsh node1.private.net -r rsh /pub/g03/linda-exe/l302.exel 15728640 transstilbene.chk 1 /home/user/g03test/Gau-4924.int 0 /home/user/g03test/Gau-4924.rwf 0 /home/user/g03test/Gau-4924.d2e 0 /home/user/g03test/Gau-4924.scr 0 /home/user/g03test/Gau-4923.inp 0 junk.out 0 +LARGS 3 1 -maxworkers 2 -chdir /home/user/g03test -worker cluster1.private.net:9497 -workerwait 900 -tsnetref 1 -nodename node1.private.net ntsnet: starting 1 worker on node2.private.net /pub/g03/linda7.1/intel-linux2.4/bin/linda_rsh node2.private.net -r rsh /pub/g03/linda-exe/l302.exel 15728640 transstilbene.chk 1 /home/user/g03test/Gau-4924.int 0 /home/user/g03test/Gau-4924.rwf 0 /home/user/g03test/Gau-4924.d2e 0 /home/user/g03test/Gau-4924.scr 0 /home/user/g03test/Gau-4923.inp 0 junk.out 0 +LARGS 3 2 -maxworkers 2 -chdir /home/user/g03test -worker cluster1.private.net:9497 -workerwait 900 -tsnetref 2 -nodename node2.private.net ntsnet: exec'ing /pub/g03/linda7.1/intel-linux2.4/bin/LindaLauncher One-electron integrals computed using PRISM. eval server 0 on cluster1.private.net has dropped it's connection. subprocess pid = 4928 has exited. status = 0x000b, id = 0, state = 17. command was /pub/g03/linda7.1/intel-linux2.4/bin/linda_sh /pub/g03/linda-exe/l302.exel 15728640 transstilbene.chk 1 /home/user/g03test/Gau-4924.int 0 /home/user/g03test/Gau-4924.rwf 0 /home/user/g03test/Gau-4924.d2e 0 /home/user/g03test/Gau-4924.scr 0 /home/user/g03test/Gau-4923.inp 0 junk.out 0 +LARGS 1 cluster1.private.net 192.168.0.101 39067 2 1 . died after signing in successfully 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