From chemistry-request@ccl.net Wed May 19 20:42:02 2004 Received: from smtp3.es.uci.edu (smtp3.es.uci.edu [128.200.80.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4K1g0La020265 for ; Wed, 19 May 2004 20:42:01 -0500 Received: from [10.0.2.2] (dhcp-204227.bio.uci.edu [128.200.204.227]) by smtp3.es.uci.edu (8.12.8/8.12.8) with ESMTP id i4K1iUa0004036; Wed, 19 May 2004 18:44:31 -0700 User-Agent: Microsoft-Entourage/10.1.4.030702.0 Date: Wed, 19 May 2004 18:44:34 -0700 Subject: Re: CCL:Question regarding Mac G5 performance From: Mengjuei Hsieh To: , CC: Ray Luo Message-ID: In-Reply-To: <40AACB95.4030705~at~uci.edu> Mime-version: 1.0 Organization: University of California, Irvine Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=-0.5 required=7.5 tests=SMILEY autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Joe, (a) Yes, it's possible. MPICH share memory works though it sucks. People in the apple scitech community normally suggest LAM/MPI instead. (b) You've better have IBM XL C/C++ and FORTRAN compiler (c) Yes and No. XL compiler optimizes better than AltiVec Framework when it goes to double. But AltiVec's framework helps GNU compiler a lot. I would suggest you to check the customized quote from Apple representatives. For the benchmark, see http://apple.sysbio.info/~mjhsieh/archives/000334.html Best, -- Mengjuei Hsieh, Luo group, Molecular Biology and Biochemistry, University of California Irvine. Tel: 49562, Address: 3144 Natural Science I building, UCI, Irvine CA 92697-3900. Group Homepage: http://rayl0.bio.uci.edu/ On 19 May 2004 12:06:49, Joe M Leonard at jle~at~world.std.com wrote: > Folks, has anybody run QM or MD benchmarks on a dual-processor > 2GHz G5 that they care to share? I'm particularly interested > in how they stack up to the newest/newer Opteron and Pentium4 > machines. If you've worked with the newer Mac's, (a) is it > possible to get good, useful 2x processor performance for > double-precision code? (b) what compilers are required to get > (a)? (c) is Altivec useful for double-precision code, or > merely for int/float work? > > A quick glance at apple.com suggests these machines go for about > $3200 USD, which isn't that different from numbers gained from a > quick glance at dell.com. I know IBM chips were number-crunchers > in the good old days, and I assume that's still the case now (which > is why I'm looking to CCL for guidance :-). > Thanks in advance! > Joe Leonard > jle~at~theworld.com From chemistry-request@ccl.net Wed May 19 17:18:57 2004 Received: from proxy1.uh.cu (smtp1.uh.cu [200.55.139.212]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JMIots012819 for ; Wed, 19 May 2004 17:18:52 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by proxy1.uh.cu (Postfix) with ESMTP id D3C252FF34; Wed, 19 May 2004 18:23:02 -0400 (CDT) Received: from fq.uh.cu (unknown [192.168.3.4]) by proxy1.uh.cu (Postfix) with ESMTP id 9C1262FE88; Wed, 19 May 2004 18:23:02 -0400 (CDT) Received: from fq.uh.cu (IDENT:1067@localhost [127.0.0.1]) by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id i4JMIXL5028281; Wed, 19 May 2004 18:18:33 -0400 Received: from localhost (rachel@localhost) by fq.uh.cu (8.12.4/8.12.4/Submit) with ESMTP id i4JMIVa8028278; Wed, 19 May 2004 18:18:31 -0400 Date: Wed, 19 May 2004 18:18:31 -0400 (CDT) From: Rachel Crespo Otero To: chemistry_at_ccl.net Cc: jlabanow_at_nd.edu Subject: Aminoacid-nucleotide interaction Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_RDNS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Does anybody know about aminoacid -nucleotide interaction calculations by quantum mechanic methods? Can help with some references? Thank you Rachel From chemistry-request@ccl.net Wed May 19 15:16:51 2004 Received: from mx5.net.nih.gov (mailfwd.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JKGots007003 for ; Wed, 19 May 2004 15:16:50 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i4JKJVqB018062 for ; Wed, 19 May 2004 16:19:31 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i4JKJVd3018056; Wed, 19 May 2004 16:19:31 -0400 Date: Wed, 19 May 2004 16:13:22 -0400 From: Rick Venable To: Mike McCallum cc: Joe M Leonard , chemistry:at:ccl.net Subject: Re: CCL:Question regarding Mac G5 performance In-Reply-To: Message-ID: References: <200405191206.i4JC6nfI028466:at:world.std.com> ReplyTo: Rick_Venable:at:nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Wed, 19 May 2004, Mike McCallum wrote: > The built-in Gigabit enet is attractive, also, as charmm and NAMD > scale very well with gigabit, and it makes myrinet less > price-effective (when used on any platform, wintel included, see > http://biobos.nih.gov/apps/charmm/charmmdoc/Bench/c30b1.html for > example). I decided that dual G5 xserve cluster nodes with gigabit > switches were much more cost-effective for me than any other > processor, especially any high-bandwidth specialty comm method > (apple's gigabit has a pretty low latency also). Having run the CHARMM benchmarks cited above, I'd disagree that they suggest Gigabit is a viable alternative to Myrinet for CHARMM calculations; in fact, they suggest that Gigabit isn't much better than 100baseT, but doesn't degrade as badly for 8 processors on 4 nodes. The performance gain is so marginal that site policy is to recommended using only Myrinet for calculations with more than 2 processors. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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:at:nih.gov ALT email: rvenable:at:speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Wed May 19 16:01:35 2004 Received: from prserv.net (asmtp2.prserv.net [32.97.166.52]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4JL1Yts009201 for ; Wed, 19 May 2004 16:01:34 -0500 Received: from goofy (dhcp065-029-074-207.indy.rr.com[65.29.74.207]) by prserv.net (asmtp2) with SMTP id <200405192104112520477c7ue> (Authid: jmmckel); Wed, 19 May 2004 21:04:11 +0000 Message-ID: <001001c43de4$c65259a0$a1ce1a8f@goofy> From: "John McKelvey" To: "Ohyun Kwon" , References: Subject: Re: CCL:transition dipole moment by TDDFT Date: Wed, 19 May 2004 16:03:45 -0500 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 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=4.1 required=7.5 tests=MAILTO_TO_SPAM_ADDR, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Wild idea proposed... What about the possibility of taking the natural orbitals of each state, Get multiplied by the square root of the respective occupation numbers, and then divide by SQRT(2+2)?... or something similar? My $.02 ... worth less and less with time.... John McKelvey ----- Original Message ----- From: "Ohyun Kwon" To: Sent: Wednesday, May 19, 2004 11:32 AM Subject: CCL:transition dipole moment by TDDFT > Dear CClers' > I would like to ask a question about how to calculate transition dipole > moments between electronic states (between ground state and excite states > or between excited state and exicted state). > Some papers address that transtion dipole moments or exicted state dipole > moments can be calculated by TDDFT using Gaussian98 or G04 programs. > I would greatly appreciate it if anyone would kindly answer, comment, or > address about this issue clearly. > I will summarize all answere I will have. > Thank you very much for your time. > > Best wishes, > > > Tommy Ohyun Kwon, Ph.D > School of Chemistry and Biochemistry > Georgia Institute of Technology > Atlanta Georgia, 30332 > Email: ohyun.kwon$at$chemistry.gatech.edu > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$at$ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu May 20 03:51:53 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4K8ppLa005756 for ; Thu, 20 May 2004 03:51:52 -0500 Received: by leitl.org (Postfix, from userid 500) id D2D733A80D3; Thu, 20 May 2004 10:54:33 +0200 (CEST) Date: Thu, 20 May 2004 10:54:33 +0200 From: Eugen Leitl To: chemistry-.at.-ccl.net Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance (fwd from mmccallum-.at.-pacific.edu) (fwd from bill-.at.-cse.ucdavis.edu) Message-ID: <20040520085433.GZ16732-.at.-leitl.org> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="PaACFu8FWA0UZxdw" Content-Disposition: inline User-Agent: Mutt/1.4i X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_2, MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --PaACFu8FWA0UZxdw Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable ----- Forwarded message from Bill Broadley ----- From: Bill Broadley Date: Wed, 19 May 2004 15:13:32 -0700 To: Eugen Leitl Cc: Beowulf-.at.-beowulf.org Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance (fwd from = mmccallum-.at.-pacific.edu) User-Agent: Mutt/1.4.1i > I had done some comparisons between price/performance, and I found dual = =20 > G5s to be at or near the best in price/performance, especially if =20 > things are recompiled with the IBM compilers (between 8-10 % speed =20 > increase over pre-compiled (with apple gcc) versions of NAMD2, and =20 > using standard gcc for charmm). I would expect that things like =20 > gaussian03 run very well (I believe gaussian uses the IBM compilers for = =20 > macOS). For MD, the speedup seems to be due to the on-chip square root = =20 > eval. Any actual numbers would be very useful, ideally with the compilers, compiler options, motherboard, and similar. Did you compare 1 job per node vs 1 job per node? Or 2 jobs per node vs 2 jobs per node? 4 or 8 dimms? Which kind of memory PC2700? PC3200? > The built-in Gigabit enet is attractive, also, as charmm and NAMD scale = =20 > very well with gigabit, and it makes myrinet less price-effective (when = =20 > used on any platform, wintel included, see > http://biobos.nih.gov/apps/charmm/charmmdoc/Bench/c30b1.html for =20 > example). I decided that dual G5 xserve cluster nodes with gigabit =20 I come to a different conclusion based on those graphs. In the first graph myrinet improves by a factor of 2.6 (250 -> 95 seconds) from 2 processors to 8, where gige improves by only 20% (255 -> 210). In the second graph gigE gets SLOWER from 2 to 8 processors. Do you think in either case the 8 node (let alone 16) gige cluster would have better price/performance then a myrinet cluster? Seems like for applications like shown on that page you shouldn't really bother with a cluster over 2 nodes with gigE, not many people would be willing to pay a factor of 4 more for 20% or even negative scaling. > switches were much more cost-effective for me than any other processor, = =20 Cost effective =3D price/performance? Can you make any numbers available? > especially any high-bandwidth specialty comm method (apple's gigabit =20 > has a pretty low latency also). Oh? Can you share the apple gigabit numbers? What is "pretty low"? > Additional considerations for us were the BSD environment which is more = =20 > secure than windows, and the OS is arguably more stable and supported =20 I'd agree with more stable and supported for use as a desktop, I'd disagree with stable and supported as computational node. OSX is the new player on the block in this space. Do you really think you would get a good response from calling apple's tech support line when the scheduler or network stack isn't performing to your performance expectations? =20 Certainly a very reasonable thing. > It is my impression that opterons, PIVs, G5s all have their advantages, = =20 Agreed, thus the value in sharing performance actual results for specific codes in specific environments. --=20 Bill Broadley Computational Science and Engineering UC Davis ----- End forwarded message ----- --=20 Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net --PaACFu8FWA0UZxdw Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.2-rc1-SuSE (GNU/Linux) iD8DBQFArHJJdbAkQ4sp9r4RApiFAKCtOliCSe2MVg6sg38ar+5bqgCuaQCgp6ik zZk3e6daK/goQCcefXpq8KE= =uZfR -----END PGP SIGNATURE----- --PaACFu8FWA0UZxdw-- From chemistry-request@ccl.net Thu May 20 05:14:10 2004 Received: from leitl.org (leitl.org [217.172.178.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4KAE9La009906 for ; Thu, 20 May 2004 05:14:09 -0500 Received: by leitl.org (Postfix, from userid 500) id 078073A80D3; Thu, 20 May 2004 12:16:48 +0200 (CEST) Date: Thu, 20 May 2004 12:16:48 +0200 From: Eugen Leitl To: chemistry{at}ccl.net Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance (fwd from mmccallum{at}pacific.edu) (fwd from hunting{at}ix.netcom.com) Message-ID: <20040520101648.GJ16732{at}leitl.org> Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="mVonZaCXjkyW6e25" Content-Disposition: inline User-Agent: Mutt/1.4i X-Spam-Status: No, hits=1.3 required=7.5 tests=HTML_MESSAGE,IMPRONONCABLE_2, MK_BAD_HTML_04 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --mVonZaCXjkyW6e25 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable See http://leitl.org/Benchmark.daresbury.pdf http://leitl.org/compchem.pdf for files mentioned in below message. ----- Forwarded message from Michael Huntingdon ---= -- From: Michael Huntingdon Date: Wed, 19 May 2004 23:05:12 -0700 To: Bill Broadley , Eugen Leitl Cc: Beowulf{at}beowulf.org Subject: Re: [Beowulf] CCL:Question regarding Mac G5 performance (fwd from mmccallum{at}pacific.edu) X-Mailer: QUALCOMM Windows Eudora Version 6.0.3.0 I've spent some time sifting through the attached numbers. Though not each= =20 lends itself to hp Itanium 2, there appears to be a very balanced trend.=20 For clusters, scale down the hp rx2600 to the rx1600 dual CPU with fewer=20 PCI-X slots, comparable performance, HP-UX/linux/OVMS, in box upgrades,=20 excellent services, and education price under $3,000. I'm at a loss as to why there is not a great deal more conversation around= =20 these systems. hptc clusters should lend themselves to easy additions and= =20 upgrades. An investment in Pentuim, SPARC, Athlon, or Opteron yesterday,= =20 should easily include G5, Itanuim 2 or futures toward cluster enhancements.= =20 =46rom the attachments, it looks to me as though the Itanium 2 numbers are= =20 (at least) compelling, with a long term commitment to the hardware=20 technology as well as the operating systems. Cheers Michael At 03:13 PM 5/19/2004, Bill Broadley wrote: >> I had done some comparisons between price/performance, and I found dual >> G5s to be at or near the best in price/performance, especially if >> things are recompiled with the IBM compilers (between 8-10 % speed >> increase over pre-compiled (with apple gcc) versions of NAMD2, and >> using standard gcc for charmm). I would expect that things like >> gaussian03 run very well (I believe gaussian uses the IBM compilers for >> macOS). For MD, the speedup seems to be due to the on-chip square root >> eval. > >Any actual numbers would be very useful, ideally with the compilers, >compiler options, motherboard, and similar. Did you compare 1 job per >node vs 1 job per node? Or 2 jobs per node vs 2 jobs per node? 4 or 8 >dimms? Which kind of memory PC2700? PC3200? > >> The built-in Gigabit enet is attractive, also, as charmm and NAMD scale >> very well with gigabit, and it makes myrinet less price-effective (when >> used on any platform, wintel included, see >> http://biobos.nih.gov/apps/charmm/charmmdoc/Bench/c30b1.html for >> example). I decided that dual G5 xserve cluster nodes with gigabit > >I come to a different conclusion based on those graphs. In the first >graph myrinet improves by a factor of 2.6 (250 -> 95 seconds) from 2 >processors to 8, where gige improves by only 20% (255 -> 210). In the >second graph gigE gets SLOWER from 2 to 8 processors. Do you think in >either case the 8 node (let alone 16) gige cluster would have better >price/performance then a myrinet cluster? > >Seems like for applications like shown on that page you shouldn't >really bother with a cluster over 2 nodes with gigE, not many people >would be willing to pay a factor of 4 more for 20% or even negative >scaling. > >> switches were much more cost-effective for me than any other processor, > >Cost effective =3D price/performance? Can you make any numbers available? > >> especially any high-bandwidth specialty comm method (apple's gigabit >> has a pretty low latency also). > >Oh? Can you share the apple gigabit numbers? What is "pretty low"? > >> Additional considerations for us were the BSD environment which is more >> secure than windows, and the OS is arguably more stable and supported > >I'd agree with more stable and supported for use as a desktop, I'd >disagree with stable and supported as computational node. OSX is the >new player on the block in this space. Do you really think you would >get a good response from calling apple's tech support line when the >scheduler or network stack isn't performing to your performance >expectations? > >Certainly a very reasonable thing. > >> It is my impression that opterons, PIVs, G5s all have their advantages, > >Agreed, thus the value in sharing performance actual results for >specific codes in specific environments. > >-- >Bill Broadley >Computational Science and Engineering >UC Davis >_______________________________________________ >Beowulf mailing list, Beowulf{at}beowulf.org >To change your subscription (digest mode or unsubscribe) visit=20 >http://www.beowulf.org/mailman/listinfo/beowulf ********************************************************************* Systems Performance Consultants Michael Huntingdon Higher Education Technology Office (408) 294-6811 131-A Stony Circle, Suite 500 Cell (707) 478-0226 Santa Rosa, CA 95401 fax (707) 577-7419 Web:=20 <http://www.spcnet.com>=20 hunting{at}ix.netcom.com ********************************************************************* ----- End forwarded message ----- --=20 Eugen* Leitl leitl ______________________________________________________________ ICBM: 48.07078, 11.61144 http://www.leitl.org 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE http://moleculardevices.org http://nanomachines.net --mVonZaCXjkyW6e25 Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.2-rc1-SuSE (GNU/Linux) iD8DBQFArIWQdbAkQ4sp9r4RApSEAKCgU2LNlWbDvvwZ3myYs3PK00YjcgCdHSAP zLofvTqyaembnl4Xoj2uS40= =lju9 -----END PGP SIGNATURE----- --mVonZaCXjkyW6e25-- From chemistry-request@ccl.net Thu May 20 03:22:32 2004 Received: from bells.cs.ucl.ac.uk (bells.cs.ucl.ac.uk [128.16.5.31]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i4K8MULa004402 for ; Thu, 20 May 2004 03:22:31 -0500 Received: from modem-1544.chameleon.dialup.pol.co.uk by bells.cs.ucl.ac.uk with UK SMTP id ; Thu, 20 May 2004 09:24:52 +0100 Message-ID: <002a01c43e43$a17c10d0$085686d9$at$cs.ucl.ac.uk> From: Marialuisa Pellegrini-Calace To: Baoqiang Cao , chemistry References: <1084981318.2869.1.camel$at$dhcp-539-820.geop.uc.edu> Subject: Re: CCL:The hydrophocities for 20 amino acids Date: Thu, 20 May 2004 09:21:35 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1409 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Cao, I'm aware of 2 experimental scales that can be used a measure of the hydrophobicity for the 20 amino acids: 1) the experimental water-phosphatidylcholine micelles and water-n-octanol partition coefficients; the reference is: White SH, Wimley WC. Hydrophobic interactions of peptides with membrane interfaces. Biochim Biophys Acta 1998;1376:339-352. 2) the turn propensity scale, that is calculated by an experimental system for the analysis of turn formation in a single 40 amino acid long poly(L) TMH embedded in the membrane of the endoplasmic reticulum. The reference is : Monne M, Hermasson M, von Heijne G, A turn propensity scale for transmembrane helices. J Mol Biol 1999;288:141-145. Cheers, Marialuisa ___________________________________ Marialuisa Pellegrini-Calace, PhD European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton CB10 1SD Cambridge (UK) E-mail: marial$at$ebi.ac.uk Tel: +44 (0)1223 492543 Fax: +44 (0)1223 494468 ___________________________________ ----- Original Message ----- From: "Baoqiang Cao" To: Sent: Wednesday, May 19, 2004 4:46 PM Subject: CCL:The hydrophocities for 20 amino acids > Dear CCL members, > > I need the experimental results of the hydrophobicities for 20 amino > acids, could you please show me how I can get them? Any tips will be > welcome! > > Best, > Cao > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY$at$ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST$at$ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jlabanow$at$nd.edu (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu May 20 09:40:55 2004 Received: from CLEMSON.EDU (mail.clemson.edu [130.127.28.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i4KEeqvg026079 for ; Thu, 20 May 2004 09:40:52 -0500 Received: from venus.clemson.edu (rhodes153dhcp156.ces.clemson.edu [130.127.153.156]) by CLEMSON.EDU (8.12.11/8.12.8) with ESMTP id i4KEhU7k015107 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT); Thu, 20 May 2004 10:43:30 -0400 (EDT) Message-Id: <5.2.1.1.2.20040520103712.025c24a8^at^mail.clemson.edu> X-Sender: sun^at^mail.clemson.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Thu, 20 May 2004 10:42:23 -0400 To: Baoqiang Cao , chemistry^at^ccl.net From: "Yu Sun (Denis)" Subject: Re: CCL:The hydrophocities for 20 amino acids In-Reply-To: <1084981318.2869.1.camel^at^dhcp-539-820.geop.uc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Spam-Level: X-Scanned-By: MIMEDefang 2.43 X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net In the paper: J. Chromatography A. 978(2002) 71-79, more than 40 different hydrophobicity scales were classified. Some based on Gibbs free energy of transfer and retention time in HPLC. You may find the literature cited in that paper useful. Denis At 11:46 AM 5/19/2004 -0400, Baoqiang Cao wrote: >Dear CCL members, > >I need the experimental results of the hydrophobicities for 20 amino >acids, could you please show me how I can get them? Any tips will be >welcome! > >Best, > Cao > > > > >-= This is automatically added to each message by the mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY^at^ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST^at^ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jlabanow^at^nd.edu (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+