From owner-chemistry@ccl.net Tue Mar 25 07:24:00 2008 From: "Julien Lefeuvre j.lefeuvre_._iecb.u-bordeaux.fr" To: CCL Subject: CCL: problem linking GAMESS Message-Id: <-36540-080325063321-31753-+4ZjaptIjBvKQ6Z7i0CcvQ=server.ccl.net> X-Original-From: Julien Lefeuvre Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 25 Mar 2008 11:32:46 +0100 MIME-Version: 1.0 Sent to CCL by: Julien Lefeuvre [j.lefeuvre~!~iecb.u-bordeaux.fr] 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 García Hello Victor, I installed successfully Gamess-US on a Ubuntu 7.10 64 bits using build-env, gfortran and atlas from the repositories (atlas3-base, atlas3-base-dev, atlas3-headers). Here is the log of the installation process (inspired from http://www.webmo.net/support/gamess_linux.html ): ########################################### cd /opt cp /home/SampleUser/gamess-current.tar.gz . tar -zxf gamess-current.tar.gz rm gamess-current.tar.gz chown -R root:root gamess/ chmod -R ugo+rx gamess/ cd gamess/ sed -e 's_/u1/mike/gamess_/opt/gamess_g' -e 's_set TARGET=ibm64_set TARGET=linux64_g' comp > comp.new sed -e 's_/u1/mike/gamess_/opt/gamess_g' -e 's_set TARGET=ibm64_set TARGET=linux64_g' compall > compall.new sed -e 's_/u1/mike/gamess_/opt/gamess_g' -e 's_set TARGET=ibm64_set TARGET=linux64_g' lked > lked.new sed -e 's_/u1/mike/gamess_/opt/gamess_g' -e 's_set TARGET=ibm64_set TARGET=linux64_g' runall > runall.new sed -e 's_set SCR=/scr/$USER_set SCR=/tmp_g' -e 's_~mike/gamess/_/opt/gamess/_g' -e 's_set GMSPATH=/cu/mike/gamess_set GMSPATH=/opt/gamess_g' rungms > rungms.new chmod +x *.new for scriptfile in `ls *.new | cut -d. -f1`; do mv $scriptfile.new $scriptfile ; done cd tools/ sed '/^*UNX/ s_*UNX_ _g' actvte.code > actvte.f g77 -o actvte.x actvte.f cd .. ./compall &> compall.log cd ddi/ sed -e 's_set TARGET = ibm64_set TARGET = linux64_g' compddi > compddi.new chmod +x compddi.new mv compddi.new compddi ./compddi &> compddi.log cp -p ddikick.x ../ cd .. sed 's_set ATLASPATH=/usr/lib64/atlas_set ATLASPATH=/usr/lib64_g' lked > lked.new chmod +x lked.new mv lked.new lked ./lked gamess 00 &> lked.log ################################################## HIH Julien Lefeuvre From owner-chemistry@ccl.net Tue Mar 25 08:01:01 2008 From: "Noel M O Boyle baoilleach||gmail.com" To: CCL Subject: CCL: Change Stereocenter specifically Message-Id: <-36541-080325075614-32032-8CYoqGM3wqANpczOnkKPNA||server.ccl.net> X-Original-From: "Noel M O Boyle" Date: Tue, 25 Mar 2008 07:56:09 -0400 Sent to CCL by: "Noel M O Boyle" [baoilleach()gmail.com] If you can describe the matching stereocenter by a SMARTS pattern, you can write a Python script using OpenBabel to do what you want. An example script is shown below. For more information see http://openbabel.org/wiki/Python, or the recent paper, http://dx.doi.org/10.1186/1752-153X-2-5 import pybel smarts = pybel.Smarts("C[C[#]](O)CC(=O)O") inverse = pybel.Smarts("C[C[#][#]](O)CC(=O)O") outputfile = pybel.Outputfile("sdf", "output.sdf") for mol in pybel.readfile("smi", "3_p0.smi"): matches = smarts.findall(mol) if matches: firstmatch = matches[0] matchingatom = firstmatch[1] mol.OBMol.GetAtom(matchingatom).SetClockwiseStereo() assert inverse.findall(mol), "Hasn't been inverted!" outputfile.write(mol) outputfile.close() If you have any questions, please send an email to openbabel-scripting[#]lists.sf.net. Regards, Noel > "reaz uddin riaasuddin(-)yahoo.com" wrote: > > Sent to CCL by: "reaz uddin" [riaasuddin~~yahoo.com] > Hi, > I am wondering, if it is possible or not! > Actually, I am looking for any program which can specifically change or invert the stereocenter. I have a lot of compounds to work with. All those compounds have more than one stereocenters. I want to invert one stereocenter which is common in all compounds. > So, precisely, my problem is to change a carbon's stereocenter from "S" to "R" and need to do this thing for all of compounds in database. > I know about sybyl option of invert chirality but its very time consuming. I also know the flipper from openeyes, but as far I understand, it doesn't help in this situation. > Does any body have an idea ?? > I appreciate for your time. > Thanks > REAZ > > Research Scholar > Department of Medicinal Chemistry and Pharmacognosy, > College of Pharmacy, (M/C 781) > University of Illinois at Chicago > 833 S. Wood St. > Chicago, IL 60612 > Email: ruddin(-)uic.edu, riaasuddin(-)yahoo.com > Web: http://medchem.pharm.uic.edu/ > > From owner-chemistry@ccl.net Tue Mar 25 15:00:00 2008 From: "Aleksandra Rudnitskaya aleksandra.rudnit001,,umb.edu" To: CCL Subject: CCL: pqsmol Message-Id: <-36542-080325142754-19322-ymKuwTxjX+A+Xj20NYixJA ~~ server.ccl.net> X-Original-From: "Aleksandra Rudnitskaya" Date: Tue, 25 Mar 2008 14:27:51 -0400 Sent to CCL by: "Aleksandra Rudnitskaya" [aleksandra.rudnit001=umb.edu] Hi, dear members of CCL, Does anyone deal with PQSmol? Do you know how to find transition state there? I saw only two options: 1) Single point energy, and 2) Geometry optimization. Where are the transition state options? Any suggestions are appreciated. Best regards. Alex From owner-chemistry@ccl.net Tue Mar 25 16:30:00 2008 From: "Konstantin Kudin konstantin_kudin:_:yahoo.com" To: CCL Subject: CCL:G: Boys localization in Gaussian & GAMESS - request for reference Message-Id: <-36543-080325160615-21221-NoAsCqW8t55DWgUTMe1OYg : server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 25 Mar 2008 12:05:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin:-:yahoo.com] All, Both Gaussian & GAMESS have used or are using a Boys orbital localization subroutine that started out as "QCPE program 354": QCPE Program Number: 354 Program Title: LOCAL: Boys' Localization Routine Author: Donald Boerth, Joseph A. Hashmall and Andrew Streitwieser, Jr. University of California Berkeley, California 94720 Recommended Citation: A. Streitwieser et al., QCPE 11, 354 (1978) Description: This program is to be used with a CDC version of Gaussian 70. It should be easily adaptable to the many IBM versions. Could anyone point me to a reference that described this particular implementation in detail, or at least, clearly outlined this approach? Thanks! Konstantin ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ From owner-chemistry@ccl.net Tue Mar 25 17:04:00 2008 From: "Roman D Gorbunov rgorbuno]^[aecom.yu.edu" To: CCL Subject: CCL:G: Cannot allocate memory for Gaussian. Message-Id: <-36544-080325165123-2110-0ty7gEKGZISni6/EAg+nZw(_)server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Tue, 25 Mar 2008 16:51:20 -0400 Sent to CCL by: "Roman D Gorbunov" [rgorbuno++aecom.yu.edu] Dear CCL Subscribers, I try to allocate memory for the Gaussian program (I put "%mem=3000MB" in the Gaussian input file). As the result I get: galloc: could not allocate memory.: Cannot allocate memory It is strange since with top-command I can see the following: Mem: 4050152k total, 870400k used, 3510500k free, 98756k buffers I.e. the machine HAS the required amount of memory. Did you encounter a similar problem before? Do you know what is the cause of the problem? Thank you in advance, Roman From owner-chemistry@ccl.net Tue Mar 25 19:02:00 2008 From: "Konstantin Kudin konstantin_kudin+/-yahoo.com" To: CCL Subject: CCL:G: Boys localization in Gaussian & GAMESS - request for reference Message-Id: <-36545-080325185929-360-mm/fmo9iTJYmGhwk2EAIww-*-server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 25 Mar 2008 15:59:15 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin^yahoo.com] All, Sorry for an almost double post, but it looks like in order to avoid confusion I should promptly amend my original request. Naturally, I am aware of the papers [Boys, 1960], and [Foster&Boys, 1960] which introduced the idea of localization, and gave ideas on how to implement it. However, these references are not very specific for what I am looking for. I would like to find a more pedagogical reference that would explicitly derive the rotational angle for a two orbital rotation within the Boys' localization procedure. Ideally, the expressions would look exactly like what was implemented in "QCPE program 354". Thanks again! Konstantin > All, > > Both Gaussian & GAMESS have used or are using a Boys orbital > localization subroutine that started out as "QCPE program 354": > > QCPE Program Number: 354 > Program Title: LOCAL: Boys' Localization Routine > Author: Donald Boerth, Joseph A. Hashmall and Andrew Streitwieser, > Jr. > University of California > Berkeley, California 94720 > Recommended Citation: A. Streitwieser et al., QCPE 11, 354 (1978) > Description: > This program is to be used with a CDC version of Gaussian 70. It > should > be easily adaptable to the many IBM versions. > > Could anyone point me to a reference that described this particular > implementation in detail, or at least, clearly outlined this > approach? > > Thanks! > Konstantin ____________________________________________________________________________________ Looking for last minute shopping deals? Find them fast with Yahoo! Search. http://tools.search.yahoo.com/newsearch/category.php?category=shopping From owner-chemistry@ccl.net Tue Mar 25 19:37:01 2008 From: "zhendong zhao zzhao%x%olemiss.edu" To: CCL Subject: CCL:G: Cannot allocate memory for Gaussian. Message-Id: <-36546-080325191202-4925-uKxuO21mT4w7naKs8bEBYw-#-server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 25 Mar 2008 18:10:38 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao*|*olemiss.edu] Hi Roman, Which version your gaussian is? If it is x86 32bit version, you can not request 2GB memory per CPU. Quoted from an email from gaussian: " Since you have compiled G03 as a 32 bit application it cannot use more than 2GB on a single calculation" If you are using 64bit verion gaussian, you would not have such a limit. ZZ On Tue, 25 Mar 2008 16:51:20 -0400 "Roman D Gorbunov rgorbuno]^[aecom.yu.edu" wrote: > > Sent to CCL by: "Roman D Gorbunov" [rgorbuno++aecom.yu.edu] > Dear CCL Subscribers, > > I try to allocate memory for the Gaussian program (I put > "%mem=3000MB" in the Gaussian input file). As the result I get: > galloc: could not allocate memory.: Cannot allocate memory > > It is strange since with top-command I can see the following: > Mem: 4050152k total, 870400k used, 3510500k free, 98756k > buffers > > I.e. the machine HAS the required amount of memory. Did you encounter > a similar problem before? Do you know what is the cause of the > problem? > > Thank you in advance, > Roman > > > > -= This is automatically added to each message by the mailing script > =- 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)> > From owner-chemistry@ccl.net Tue Mar 25 21:53:00 2008 From: "Joe Leonard jleonard42*o*gmail.com" To: CCL Subject: CCL:G: Boys localization in Gaussian & GAMESS - request for reference Message-Id: <-36547-080325212035-4954-NJCERXyXLJgcOr6eoKMvog|-|server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary=Apple-Mail-5-550177883 Date: Tue, 25 Mar 2008 20:17:24 -0400 Mime-Version: 1.0 (Apple Message framework v753) Sent to CCL by: Joe Leonard [jleonard42[*]gmail.com] --Apple-Mail-5-550177883 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Wow, I never thought I would get a chance to do this... While I am unfamiliar with the code in question, I did my PhD work on localized orbitals. Perhaps one of these two papers might have the equations you seek? Leonard, Luken, Int. J. Quant. Chem. 25, 355-365(1984) Leonard, Luken, Theoret. Chim. Acta 62, 107-132(1982) Failing that, you might be able to dredge them out of my dissertation if it's available electronically. "I. Quadratically convergent localized orbitals II. Open-shell SCF as a special case of the saddle-point variational method". Some of the equations might be contained in the first part. As I recall, I worked from the Foster/Boys papers, along with those of Edmiston/ Rudenberg. There's code buried in the back of the dissertation that generates the first- and second-order LMO's. Joe Leonard jleonard42-$-gmail.com On Mar 25, 2008, at 6:59 PM, Konstantin Kudin konstantin_kudin+/- yahoo.com wrote: > > Sent to CCL by: Konstantin Kudin [konstantin_kudin^yahoo.com] > All, > > Sorry for an almost double post, but it looks like in order to avoid > confusion I should promptly amend my original request. > > Naturally, I am aware of the papers [Boys, 1960], and [Foster&Boys, > 1960] which introduced the idea of localization, and gave ideas on how > to implement it. However, these references are not very specific for > what I am looking for. > > I would like to find a more pedagogical reference that would > explicitly derive the rotational angle for a two orbital rotation > within the Boys' localization procedure. Ideally, the expressions > would > look exactly like what was implemented in "QCPE program 354". > > Thanks again! > Konstantin > > >> All, >> >> Both Gaussian & GAMESS have used or are using a Boys orbital >> localization subroutine that started out as "QCPE program 354": >> >> QCPE Program Number: 354 >> Program Title: LOCAL: Boys' Localization Routine >> Author: Donald Boerth, Joseph A. Hashmall and Andrew Streitwieser, >> Jr. >> University of California >> Berkeley, California 94720 >> Recommended Citation: A. Streitwieser et al., QCPE 11, 354 (1978) >> Description: >> This program is to be used with a CDC version of Gaussian 70. It >> should >> be easily adaptable to the many IBM versions. >> >> Could anyone point me to a reference that described this particular >> implementation in detail, or at least, clearly outlined this >> approach? >> >> Thanks! >> Konstantin > > > > > ______________________________________________________________________ > ______________ > Looking for last minute shopping deals? > Find them fast with Yahoo! Search. http://tools.search.yahoo.com/ > newsearch/category.php?category=shopping > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -- "There's a knack for catching the knuckleball that's difficult to define. You let the ball get deep, relax enough not to stab at it and if things work out according to plan, you're not on a first-name basis with the fans behind the screen." --Apple-Mail-5-550177883 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Wow, I never thought I would get a chance to do = this...

While I am unfamiliar with the code in = question, I did my PhD work on localized orbitals. =A0Perhaps one of = these two papers might have the equations you = seek?

Leonard, Luken, Int. J. Quant. Chem. 25, = 355-365(1984)
Leonard, Luken, Theoret. Chim. Acta 62, = 107-132(1982)

Failing that, you might be able = to dredge them out of my dissertation if it's available electronically. = =A0
"I. Quadratically convergent localized orbitals II. = Open-shell SCF as a special case of the saddle-point variational = method". =A0Some of the equations might be contained in the first part. = =A0As I recall, I worked from the Foster/Boys papers, along with those = of Edmiston/Rudenberg. =A0There's code buried in the back of the = dissertation that generates the first- and second-order = LMO's.

Joe Leonard
On Mar 25, 2008, at 6:59 PM, Konstantin Kudin = konstantin_kudin+/-yahoo.com wrote:

Sent to = CCL by: Konstantin Kudin [konstantin_kudin^yahoo.com]
=A0All,

=A0Sorry for an almost double = post, but it looks like in order to avoid

=A0Naturally, I am aware of the = papers [Boys, 1960], and [Foster&Boys,
1960] = which introduced the idea of localization, and gave ideas on = how
to implement it. However, these = references are not very specific for
what I am = looking for.

=A0I = would like to find a more pedagogical reference that would
explicitly derive the rotational angle for a two = orbital rotation
within the Boys' localization = procedure. Ideally, the expressions would
look = exactly like what was implemented in "QCPE program 354".

=A0Thanks again!
=A0Konstantin


=A0All,

=A0Both Gaussian & GAMESS = have used or are using a Boys orbital

QCPE Program Number: 354
Program = Title: = LOCAL: Boys' Localization Routine
= Donald Boerth, Joseph A. Hashmall and Andrew = Streitwieser,
Jr.
Berkeley, = California 94720
Recommended Citation: A. = Streitwieser et al., QCPE 11, 354 (1978)
This program is to be used with = a CDC version of Gaussian 70. It
be easily adaptable to the many = IBM versions.

=A0Could = anyone point me to a reference that described this particular
implementation in detail, or at least, clearly = outlined this
approach?

=A0Thanks!
=A0Konstantin
=



=A0 =A0 =A0 = ___________________________________________________________________= _________________
Looking for last minute shopping = deals? =A0



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"There's = a knack for catching the knuckleball that's difficult to=A0define. You = let the ball get deep, relax enough not to stab at it=A0and if things = work out according to plan, you're not on a first-name basis with the = fans behind the screen."


=
= --Apple-Mail-5-550177883--