From owner-chemistry@ccl.net Sun Feb 15 06:23:00 2009 From: "xunlei ding dingxunlei*o*gmail.com" To: CCL Subject: CCL:G: G- Stop at L103 Message-Id: <-38617-090215061245-26573-SlGYGGzN40/oWCtOOtG77g[A]server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 15 Feb 2009 19:12:25 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei/a\gmail.com] Dear Rajagopalan, Thank you for your reply! The test calculation is DFT with a basis set "171 basis functions, 322 primitive gaussians, 189 cartesian basis functions". For most cases it finishes within several hours after about 30 optimization steps. But sometimes, it stopped at L103 after some optimization steps. I think it will be at L103 forever if I don't kill it (because after more than 5hours it is still at L103). Best regards, Ding 2009/2/13 Rajagopalan S. r.subramanian- -ipc.uni-stuttgart.de : > > Sent to CCL by: "Rajagopalan S." [r.subramanian]^[ipc.uni-stuttgart.de] > Hi, i think you have to increase your computation time..how big is your > molecule? how much time did you already used for calculation? > > > xunlei ding dingxunlei#%#gmail.com wrote: >> >> Sent to CCL by: xunlei ding [dingxunlei###gmail.com] >> Dear CCLers, >> >> Sometimes the G03 jobs halt at L103 and the last two lines of the >> output file are >> " >> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad" >> and "Berny optimization.". >> The jobs will not stop unless I kill them. >> Does anybody know how to solve this problem? >> >> Best regards, >> Dinghttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Sun Feb 15 06:57:01 2009 From: "xunlei ding dingxunlei.:.gmail.com" To: CCL Subject: CCL:G: G- Stop at L103 Message-Id: <-38618-090215062118-26875-EZc6uatuoOj4crhQYtWZvw*|*server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 15 Feb 2009 19:21:05 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei=-=gmail.com] Dear Vjeran, Thank you for you reply! I did as you suggested to add #p in the input file. But no more useful information is found. The last lines of the output file is like below. -------------------------------------- SCF Done: E(UB+HF-LYP) = -867.687025251 A.U. after 4 cycles Convg = 0.1821D-04 -V/T = 3.7743 S**2 = 2.1150 KE= 3.127575236482D+02 PE=-3.514928744192D+03 EE= 1.491749062734D+03 Annihilation of the first spin contaminant: S**2 before annihilation 2.1150, after 2.0021 Leave Link 502 at Sun Feb 15 13:42:44 2009, MaxMem= 262144000 cpu: 59.4 (Enter /share/apps/gaussian/g03/l701.exe) Compute integral first derivatives. ... and contract with generalized density number 0. 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 1653 NPrTT= 7123 LenC2= 1562 LenP2D= 5704. LDataN: DoStor=F MaxTD1= 8 Len= 415 LDataN: DoStor=T MaxTD1= 8 Len= 415 Leave Link 701 at Sun Feb 15 13:42:47 2009, MaxMem= 262144000 cpu: 11.8 (Enter /share/apps/gaussian/g03/l702.exe) L702 exits ... SP integral derivatives will be done elsewhere. Leave Link 702 at Sun Feb 15 13:42:47 2009, MaxMem= 262144000 cpu: 0.0 (Enter /share/apps/gaussian/g03/l703.exe) Compute integral first derivatives, UseDBF=F. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Leave Link 703 at Sun Feb 15 13:43:04 2009, MaxMem= 262144000 cpu: 61.8 (Enter /share/apps/gaussian/g03/l716.exe) Dipole =-1.94701626D+00 1.16055147D+00 8.53878103D-01 ***** Axes restored to original set ***** ------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr) Number Number X Y Z ------------------------------------------------------------------- 1 8 0.000325302 -0.005154418 -0.003690741 2 26 -0.002860649 -0.001881006 -0.002204418 3 26 0.000116283 0.002988548 -0.001270068 4 26 -0.000765371 -0.004330111 0.001573275 5 26 0.008226724 0.005877568 0.001584660 6 26 -0.009761744 0.004207222 0.005216266 7 26 0.004719455 -0.001707803 -0.001208976 ------------------------------------------------------------------- Cartesian Forces: Max 0.009761744 RMS 0.004145189 Leave Link 716 at Sun Feb 15 13:43:04 2009, MaxMem= 262144000 cpu: 0.0 (Enter /share/apps/gaussian/g03/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. -------------------------------------- Best regards, Ding 2009/2/13 Vjeran Gomzi : > Perhaps some more information could be obtained using the #P keyword in the > job route? If you already have done so and the output is as quoted, then I'm > afraid > I can't help. > > Sincerely, > > Vjeran Gomzi, PhD > > DOCB/QOCG > Rudjer Boskovic Institute > Bijenicka c 54 > HR-10000 Zagreb > CROATIA, Europe > > Qouting "xunlei ding dingxunlei#%#gmail.com" : > >> >> Sent to CCL by: xunlei ding [dingxunlei###gmail.com] >> Dear CCLers, >> >> Sometimes the G03 jobs halt at L103 and the last two lines of the >> output file are >> " >> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad" >> and "Berny optimization.". >> The jobs will not stop unless I kill them. >> Does anybody know how to solve this problem? >> >> Best regards, >> Ding>> >> >> > > > -- From owner-chemistry@ccl.net Sun Feb 15 12:29:01 2009 From: "Alexander Kos software=akosgmbh.eu" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38619-090215112629-24162-tspRN1Lcnw1FePDdDEGiIw()server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 15 Feb 2009 16:11:18 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software:-:akosgmbh.eu] Pipeline Pilot is a great product, but for some people not affordable. A cheaper option is KNIME and Cheshire from Symyx. Cheshire is a low cost product that must be installed for several of the better = chemoinformatics applications. On www.symyx.com you will find some nodes that might be helpful. A more or less automated lead finding application that works by = clustering compounds of similar biological activity, but not necessarily similar by structure. Please have a look at wwww.akosgmbh.de/cwm and follow the = links to CWM Lead Finder. With best regards, Alex AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067=20 Fax (to mail):=A0=A0 +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software^-^akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, = General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. (www.symyx.com), DIMENSION = 5, Ltd. (www.miner3d.com), CompuDrug International (www.compudrug.com), Molecular Networks GmbH (www.mol-net.de), and others. =20 -----Original Message----- > From: owner-chemistry+software=3D=3Dakosgmbh.eu^-^ccl.net [mailto:owner-chemistry+software=3D=3Dakosgmbh.eu^-^ccl.net] On Behalf Of = Igor Filippov Contr igorf#%#helix.nih.gov Sent: Freitag, 13. Februar 2009 14:55 To: Kos, Alexander J. Subject: CCL: Chemical library analysis tool Sent to CCL by: "Igor Filippov [Contr]" [igorf-.-helix.nih.gov] Pipeline Pilot http://accelrys.com/products/scitegic/ Cheers, Igor On Fri, 2009-02-13 at 06:25 -0500, Sangeetha Vimal srdshigella-x-gmail.com wrote: > Sent to CCL by: "Sangeetha Vimal" [srdshigella,gmail.com] > Hi all, >=20 > Can someone suggest me a chemical library analysis tool, which can = help in clustering/diversity analysis of chemical compounds in the database.=20 >=20 > Thanks > Sangeetha>=20 --=20 Igor Filippov [Contr] -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Feb 15 13:03:01 2009 From: "Alexander Kos software+*+akosgmbh.eu" To: CCL Subject: CCL: sources for experimental pKa data Message-Id: <-38620-090215112616-24107-fSfG2QvFy/lvDJnqLzkWdA_-_server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 15 Feb 2009 16:26:23 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software__akosgmbh.eu] MDL, now Symyx Technologies Inc, had a databases with pKa values o = ca.40'000 compounds. However, I don't know what happened with the database. If you = are interested, please contact me. With best regards, Alex AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067=20 Fax (to mail):=A0=A0 +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software!=!akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, = General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. (www.symyx.com), DIMENSION = 5, Ltd. (www.miner3d.com), CompuDrug International (www.compudrug.com), Molecular Networks GmbH (www.mol-net.de), and others. -----Original Message----- > From: owner-chemistry+software=3D=3Dakosgmbh.eu!=!ccl.net [mailto:owner-chemistry+software=3D=3Dakosgmbh.eu!=!ccl.net] On Behalf Of = Attila Tajti tat],[chem.elte.hu Sent: Freitag, 13. Februar 2009 18:17 To: Kos, Alexander J. Subject: CCL: sources for experimental pKa data Sent to CCL by: "Attila Tajti" [tat^^chem.elte.hu] Dear All, for the design of an alternative theoretical approach for pKa = prediction, I am looking for an easy-to-process, public or commercial database of experimental pKa values with the highest possible number of entries and level of chemical diversity. Text-based formats like SDFile, would be = highly preferred.=20 Does anyone know about a source for such a DB? Thanks for any tip or suggestion! Attila Tajti tat,chem.elte.hu -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sun Feb 15 13:38:00 2009 From: "Rajagopalan S. r.subramanian_._ipc.uni-stuttgart.de" To: CCL Subject: CCL:G: G- Stop at L103 Message-Id: <-38621-090215124840-5001-EYidVbh2FcQ+02v1KhdDCQ ~ server.ccl.net> X-Original-From: "Rajagopalan S." Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sun, 15 Feb 2009 18:48:23 +0100 MIME-Version: 1.0 Sent to CCL by: "Rajagopalan S." [r.subramanian() ipc.uni-stuttgart.de] Hi, take the last geometry and restart again.. xunlei ding dingxunlei*o*gmail.com wrote: > Sent to CCL by: xunlei ding [dingxunlei/a\gmail.com] > Dear Rajagopalan, > > Thank you for your reply! > > The test calculation is DFT with a basis set "171 basis functions, > 322 primitive gaussians, 189 cartesian basis functions". > For most cases it finishes within several hours after about 30 > optimization steps. > But sometimes, it stopped at L103 after some optimization steps. > I think it will be at L103 forever if I don't kill it (because after > more than 5hours it is still at L103). > > Best regards, > Ding > > 2009/2/13 Rajagopalan S. r.subramanian- -ipc.uni-stuttgart.de > : > >> Sent to CCL by: "Rajagopalan S." [r.subramanian]^[ipc.uni-stuttgart.de] >> Hi, i think you have to increase your computation time..how big is your >> molecule? how much time did you already used for calculation? >> >> >> xunlei ding dingxunlei#%#gmail.com wrote: >> >>> Sent to CCL by: xunlei ding [dingxunlei###gmail.com] >>> Dear CCLers, >>> >>> Sometimes the G03 jobs halt at L103 and the last two lines of the >>> output file are >>> " >>> GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad" >>> and "Berny optimization.". >>> The jobs will not stop unless I kill them. >>> Does anybody know how to solve this problem? >>> >>> Best regards, >>> Dinghttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >>> >> From owner-chemistry@ccl.net Sun Feb 15 20:47:00 2009 From: "xunlei ding dingxunlei|*|gmail.com" To: CCL Subject: CCL: G- Stop at L103 Message-Id: <-38622-090215194523-3196-0vQ6yv7Ss0c1s1uTl02vTQ~!~server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 16 Feb 2009 08:45:09 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei++gmail.com] Dear Rajagopalan, Thank you! Yes, it works if I restart the job. But in a bash script, I did a series for different spin multiplicities. It should do with spin multiplicity as 1, 3, 5, 7, 9 ... one by one. But in some cases it stopped at, saying s=3, and nothing will be done untill I kill this L103. So much CPU time is wasted. I hope it could kill itself automatically if it can't overcome L103. Best regards, Ding 2009/2/16 Rajagopalan S. r.subramanian_._ipc.uni-stuttgart.de : > > Sent to CCL by: "Rajagopalan S." [r.subramanian() ipc.uni-stuttgart.de] > Hi, > take the last geometry and restart again.. From owner-chemistry@ccl.net Sun Feb 15 22:15:00 2009 From: "Jonas Baltrusaitis jasius_1*|*yahoo.com" To: CCL Subject: CCL:G: RI-MP2 fittingbasis set Message-Id: <-38623-090215221343-23571-g5ekSJORNpPB41zw5oZ2EA[a]server.ccl.net> X-Original-From: "Jonas Baltrusaitis" Date: Sun, 15 Feb 2009 22:13:38 -0500 Sent to CCL by: "Jonas Baltrusaitis" [jasius_1 _ yahoo.com] Hi, I want to use NWChem RI-MP2 for organometallic cluster geometry optimisation+frequency calculation (in comparison with some DFT functionals), since my structures depend heavily on weak interactions. However (unless one uses Turbomole based programs), the fitting basis sets are very limited (not only in NWChem). I would need something that goes up to Xe, hence transition metals involved. I am using gaussian basis sets, such as 6-311G* in combination with pseudopotentials, such as LANL2DZ. I never quite found a good fitting basis set for RI-MP2 anywhere for these basis sets. Of course, I could download those from Turbomole website, but aren't those "optimized" for slater basis sets? What is a good fitting basis set, for that matter? If I found any in the literature, how can I test with my method and primary basis set to evaluate if it's "good" fit? Howdo I define or quantify this goodness of fit? thanks Jonas Baltrusaitis University of Iowa