From owner-chemistry@ccl.net Mon Mar 24 13:03:01 2008 From: "Jerome Kieffer jerome.Kieffer%%terre-adelie.org" To: CCL Subject: CCL: Program for identifying small-molecule structure from NOE spectra Message-Id: <-36537-080324114834-19503-WyOFqSlETFGklbeeX88Ubw]=[server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 24 Mar 2008 16:49:23 +0100 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer-*-terre-adelie.org] On Thu, 22 Nov 2007 10:59:37 +0800 "Arthur computationalboy|*|gmail.com" wrote: > Dear all: > I want to identifying some small-molecule structures, mainly their absolu= te configuration from NOE spectra. Many protein entries in RCSB PDB were re= solved via this way, though they are maro molecules. > Could anyone give me some instructions on the calculation programs? NOE effect are dramatically different between small (conformationnally averaged at NMR timescale) and big macromolecules. You may be interested by LSD, a soft developped by a french university. http://helios.univ-reims.fr/Labos/UPRESA6013/LSD/index_FR.html Well this web page is in French but consider reading the publication listed on the page. Hope this helps. --=20 J=E9r=F4me KIEFFER =20 From owner-chemistry@ccl.net Mon Mar 24 19:12:00 2008 From: "Victor Manuel Rosas-Garcia quimico69||yahoo.com" To: CCL Subject: CCL: problem linking GAMESS Message-Id: <-36538-080324180553-9309-e6+lWyrMoBcfIWFhiJUD5w---server.ccl.net> X-Original-From: Victor Manuel Rosas-Garcia Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 24 Mar 2008 14:05:41 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Victor Manuel Rosas-Garcia [quimico69|*|yahoo.com] Hello everybody,=0A=0AI need some help in getting GAMESS-US to run. I'm tr= ying to install GAMESS-US (most recent version) on a 64 bit machine (AMD cp= u). My setup is as follows:=0A=0AUbuntu 7.10 for 64 bit arch=0Agcc version= 4.2.1 (installed in addition to ubuntu's default compiler: gcc 4.1.3)=0Agf= ortran 4.2.1=0Aatlas libraries v. 3.8.0 (downloaded from sourceforge, not t= he ones from the ubuntu repositories)=0A=0AI installed ATLAS first and went= through all the checks and tests. No failures there.=0AThen compiled GA= MESS. No problem there either.=0AWhen running lked, linking fails with ove= r a hundred messages similar to this one:=0A=0A/usr/local/atlas/lib/libf77b= las.so: undefined reference to 'ATL_chemv'=0A=0Aeach message pointing out a= different undefined reference.=0A=0AWhat puzzles me the most, is that I ha= ve, in the past, successfully gotten GAMESS-US to run under the 32-bit vers= ion of Ubuntu 7.10. The only major difference I can think of is that I had= never compiled ATLAS before, but I read the installation instructions care= fully, several times. And the sanity checks did not indicate anything wron= g.=0A=0ADid I miss anything obvious?=0A=0A=0AVictor M. Rosas Garc=EDa=0A=0A= =0A=0A=0A ____________________________________________________________= ________________________=0ALooking for last minute shopping deals? =0AFind= them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/cat= egory.php?category=3Dshopping From owner-chemistry@ccl.net Mon Mar 24 21:36:01 2008 From: "zhendong zhao zzhao[#]olemiss.edu" To: CCL Subject: CCL: problem linking GAMESS Message-Id: <-36539-080324202945-8599-wB81pc24DuBRxegz3oKD+Q..server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=GB2312 Date: Mon, 24 Mar 2008 18:38:19 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao*o*olemiss.edu] Hi, Check your atlas installation, make sure the final lib name is libf77blas.so, I would expect it may have a different name. Maybe you can try GotoBLAS, I know it works on ubuntu X86_64. BTW, I find gfortran 4.2 can successully compile and link gamess, but the test will fail on one/two tests. ZZ On Mon, 24 Mar 2008 14:05:41 -0700 (PDT) "Victor Manuel Rosas-Garcia quimico69||yahoo.com" wrote: > > Sent to CCL by: Victor Manuel Rosas-Garcia [quimico69|*|yahoo.com] > Hello everybody, > > I need some help in getting GAMESS-US to run. I'm trying to install > GAMESS-US (most recent version) on a 64 bit machine (AMD cpu). My > setup is as follows: > > Ubuntu 7.10 for 64 bit arch > gcc version 4.2.1 (installed in addition to ubuntu's default > compiler: gcc 4.1.3) gfortran 4.2.1 > atlas libraries v. 3.8.0 (downloaded from sourceforge, not the ones > from the ubuntu repositories) > > I installed ATLAS first and went through all the checks and tests. > No failures there. Then compiled GAMESS. No problem there either. > When running lked, linking fails with over a hundred messages similar > to this one: > > /usr/local/atlas/lib/libf77blas.so: undefined reference to 'ATL_chemv' > > each message pointing out a different undefined reference. > > What puzzles me the most, is that I have, in the past, successfully > gotten GAMESS-US to run under the 32-bit version of Ubuntu 7.10. The > only major difference I can think of is that I had never compiled > ATLAS before, but I read the installation instructions carefully, > several times. And the sanity checks did not indicate anything wrong. > > Did I miss anything obvious? > > > Victor M. Rosas Garc¨Şa > > > > > ____________________________________________________________________________________ > Looking for last minute shopping deals? > Find them fast with Yahoo! Search. > http://tools.search.yahoo.com/newsearch/category.php?category=shopping > > > > -To recover the email address of the author of the message, please > change the strange characters on the top line to the %% sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> >