From owner-chemistry@ccl.net Fri May 11 03:54:00 2007 From: "St phane Vellay stephane.vellay _ free.fr" To: CCL Subject: CCL: Tunnels in proteins Message-Id: <-34238-070511034926-10245-0/2ZtoV6qg2bZ6M3hfeuig-.-server.ccl.net> X-Original-From: "St phane Vellay" Date: Fri, 11 May 2007 03:49:22 -0400 Sent to CCL by: "St phane Vellay" [stephane.vellay{:}free.fr] Dear Maurizzio, There is CAVER, a PyMol plugin : http://loschmidt.chemi.muni.cz/caver/ Regards, Stphane | Dr Stphane VELLAY, PharmD | stephane.vellay:free.fr | http://stephane.vellay.free.fr From owner-chemistry@ccl.net Fri May 11 04:29:01 2007 From: "andrea spitaleri spitaleri.andrea#%#hsr.it" To: CCL Subject: CCL: Tunnels in proteins Message-Id: <-34239-070511041833-23031-g+bOJAsHUFZje39bJoPcpg]|[server.ccl.net> X-Original-From: andrea spitaleri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 11 May 2007 09:20:51 +0200 MIME-Version: 1.0 Sent to CCL by: andrea spitaleri [spitaleri.andrea_._hsr.it] Hi what about caver? http://loschmidt.chemi.muni.cz/caver/index.php Regards andrea Maurizzio m.argonni^^gmail.com wrote: > Hello to all, > > I was wondering if anyone is aware of a web server or free software able > to find tunnels in proteins. > The problem I want to solve is the following: given the location of the > active site in a protein I would like to know the possible routes for > substrates to get there from the exterior. > Any clues are greatly appreciated. Thanks, > > Maurizzio > -- ------------------------------- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ ------------------------------- ******************************************************************** Sostieni la ricerca del San Raffaele con il 5permille! E' SEMPLICE E NON COSTA NULLA. Basta indicare nell'apposito riquadro della dichiarazione dei redditi ("Ricerca sanitaria") il codice fiscale della Fondazione Centro S. Raffaele del Monte Tabor: 03 06 42 80 153 e ricordarsi di firmare. Se vuoi saperne di piu' scrivi a 5permille]=[hsr.it o vai sul sito www.5xmille.org From owner-chemistry@ccl.net Fri May 11 09:51:01 2007 From: "Taye Beyene Demisse sene3095_._yahoo.com" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34240-070511093926-27721-OuMcYGARiJ2Q5zBbaq6h5w!A!server.ccl.net> X-Original-From: "Taye Beyene Demisse" Date: Fri, 11 May 2007 09:39:21 -0400 Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] Hello? When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. Please suggest what to change and correct. Taye. Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 10-May-2007 ********************************************* %chk=dp[pmt-oxd-rohf.chk %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------------------- opt rob3lyp/6-31g(d) geom=connectivity ---------------------------------------- 1/14=-1,18=20,26=3,38=1,57=2/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/7=6/1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/14=-1,18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/5=5,7=6,16=3/1; 5/5=2,23=1,38=5/2; 7//1,2,3,16; 1/14=-1,18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; ------------------- Title Card Required ------------------- Symbolic Z-matrix: Charge = 1 Multiplicity = 2 ; ; ; ; ; ; Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles Convg = 0.7166D-06 -V/T = 2.0048 S**2 = 0.7500 Annihilation of the first spin contaminant: S**2 before annihilation 0.7500, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1 From owner-chemistry@ccl.net Fri May 11 10:49:01 2007 From: "Close, David M. CLOSED*|*mail.etsu.edu" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34241-070511101507-6861-+2qddkiM/kaSHNq/67bhLQ|server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 11 May 2007 10:14:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED a mail.etsu.edu] Taye: This should be easy to fix. However we need to know some more about this job. You may be close to convergence, and may merely have exceeded the number of allowed scf cycles. It would be helpful to know about some of the last scf cycles. How close were these to convergence. In the output there are 4 threshold values printed out. How many of these say YES? Also, how close are the total energies of the molecule on the last few cycles. Do you have a way of viewing the geometries of the molecule on each cycle? This can be very revealing. You have already gone 129 cycles. This is really a lot. So maybe the molecule has dissociated, or bent in some fashion that you didn't intend. Tell us more and maybe we can help. Regards, Dave Close. -----Original Message----- > From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net] Sent: Friday, May 11, 2007 9:39 AM To: Close, David M. Subject: CCL:G: DFT optimization Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] Hello? When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. Please suggest what to change and correct. Taye. Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 10-May-2007 ********************************************* %chk=dp[pmt-oxd-rohf.chk %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------------------- opt rob3lyp/6-31g(d) geom=connectivity ---------------------------------------- 1/14=-1,18=20,26=3,38=1,57=2/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/7=6/1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/14=-1,18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/5=5,7=6,16=3/1; 5/5=2,23=1,38=5/2; 7//1,2,3,16; 1/14=-1,18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; ------------------- Title Card Required ------------------- Symbolic Z-matrix: Charge = 1 Multiplicity = 2 ; ; ; ; ; ; Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles Convg = 0.7166D-06 -V/T = 2.0048 S**2 = 0.7500 Annihilation of the first spin contaminant: S**2 before annihilation 0.7500, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri May 11 11:30:00 2007 From: "Chris Moth chris.moth]~[Vanderbilt.Edu" To: CCL Subject: CCL: Tunnels in proteins Message-Id: <-34242-070510225717-8449-mvqMLjMh3OyXTz5eojmBRg*_*server.ccl.net> X-Original-From: "Chris Moth" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 10 May 2007 21:22:36 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: "Chris Moth" [chris.moth(_)Vanderbilt.Edu] You might look at: Furse, K. E.; Pratt, D. A.; Schneider, C.; Brash, A. R.; Porter, N. A.; Lybrand, T. P. "Molecular Dynamics Simulations of Arachidonic Acid-Derived Pentadienyl Radical Intermediate Complexes with COX-1 and COX-2: Insights into Oxygenation Regio- and Stereoselectivity," Biochemistry 2006, 45, 3206-3218. If the "channel_finder" utility sounds appealing, write my boss, Terry Lybrand, and I suspect he will provide you a copy of the PERL script. > Hello to all, > > I was wondering if anyone is aware of a web server or free software able > to > find tunnels in proteins. > The problem I want to solve is the following: given the location of the > active site in a protein I would like to know the possible routes for > substrates to get there from the exterior. > Any clues are greatly appreciated. Thanks, > > Maurizzio > From owner-chemistry@ccl.net Fri May 11 12:04:00 2007 From: "Herbert Fruchtl herbert.fruchtl*st-andrews.ac.uk" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34243-070511112233-7763-j4/kCW3ZZPy7I9aAJqu87w a server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 May 2007 16:21:51 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl * st-andrews.ac.uk] Your SCF did not converge. You can try SCF=QC, which will slow things down, but is more likely to converge. If you start the keyword line with #p instead of just #, you will see some convergence information (e.g. if it's nearly converged (then you could get away with, say, SCF(MaxCycle=100), or if it bounces (then use QC or experiment with damping or level shifting). Herbert Taye Beyene Demisse sene3095_._yahoo.com wrote: > Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] > Hello? > When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. > Please suggest what to change and correct. > > Taye. > > > Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 > 10-May-2007 > ********************************************* > %chk=dp[pmt-oxd-rohf.chk > %mem=6MW > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=2000MB > ---------------------------------------- > opt rob3lyp/6-31g(d) geom=connectivity > ---------------------------------------- > 1/14=-1,18=20,26=3,38=1,57=2/1,3; > 2/9=110,17=6,18=5,40=1/2; > 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4/7=6/1; > 5/5=2,38=5/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 7//1,2,3,16; > 1/14=-1,18=20/3(1); > 99//99; > 2/9=110/2; > 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4/5=5,7=6,16=3/1; > 5/5=2,23=1,38=5/2; > 7//1,2,3,16; > 1/14=-1,18=20/3(-5); > 2/9=110/2; > 6/7=2,8=2,9=2,10=2,19=2,28=1/1; > 99/9=1/99; > ------------------- > Title Card Required > ------------------- > Symbolic Z-matrix: > Charge = 1 Multiplicity = 2 > > ; > ; > ; > ; > ; > ; > Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles > Convg = 0.7166D-06 -V/T = 2.0048 > S**2 = 0.7500 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7500, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. > Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. > File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1> > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Fri May 11 12:42:00 2007 From: "Soren Eustis soren~~jhu.edu" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34244-070511120748-3059-ISmGu4jlZYbxv+m8EApnPg.:.server.ccl.net> X-Original-From: "Soren Eustis" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 11 May 2007 12:07:29 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren|jhu.edu] Try SCF=maxcycle=512 or SCF=QC. The convergence problem is SCF related and not a geometry optimization problem. SCF=QC uses the slower (~x2) quadratically convergent SCF method, but it converges more reliably. Alternatively you can just change the number of cycles from the default 128 to the max of 512. Regards, Soren Soren N. Eustis Graduate Research Assistant Department of Chemistry Johns Hopkins University Remsen Hall 3400 N Charles Street Baltimore, MD 21218 (410) 516-4675 (office) (410) 925-5167 (cell) (410) 516-8420 (fax) soren++jhu.edu -----Original Message----- > From: owner-chemistry++ccl.net [mailto:owner-chemistry++ccl.net] Sent: Friday, May 11, 2007 9:39 AM To: Eustis, Soren Subject: CCL:G: DFT optimization Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] Hello? When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. Please suggest what to change and correct. Taye. Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 10-May-2007 ********************************************* %chk=dp[pmt-oxd-rohf.chk %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------------------- opt rob3lyp/6-31g(d) geom=connectivity ---------------------------------------- 1/14=-1,18=20,26=3,38=1,57=2/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/7=6/1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/14=-1,18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/5=5,7=6,16=3/1; 5/5=2,23=1,38=5/2; 7//1,2,3,16; 1/14=-1,18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; ------------------- Title Card Required ------------------- Symbolic Z-matrix: Charge = 1 Multiplicity = 2 ; ; ; ; ; ; Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles Convg = 0.7166D-06 -V/T = 2.0048 S**2 = 0.7500 Annihilation of the first spin contaminant: S**2 before annihilation 0.7500, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri May 11 13:15:00 2007 From: "Igor Filippov Contr igorf_-_helix.nih.gov" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34245-070511123225-20215-H4GfxyatwKBbp35/necG+g|a|server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 11 May 2007 11:49:47 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf|-|helix.nih.gov] Is it a square bracket in your checkpoint filename ? Can Gaussian stomach filenames like that ? Igor On Fri, 2007-05-11 at 09:39 -0400, Taye Beyene Demisse sene3095_._yahoo.com wrote: > Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] > Hello? > When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. > Please suggest what to change and correct. > > Taye. > > > Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 > 10-May-2007 > ********************************************* > %chk=dp[pmt-oxd-rohf.chk > %mem=6MW > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=2000MB > ---------------------------------------- > opt rob3lyp/6-31g(d) geom=connectivity > ---------------------------------------- > 1/14=-1,18=20,26=3,38=1,57=2/1,3; > 2/9=110,17=6,18=5,40=1/2; > 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4/7=6/1; > 5/5=2,38=5/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 7//1,2,3,16; > 1/14=-1,18=20/3(1); > 99//99; > 2/9=110/2; > 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4/5=5,7=6,16=3/1; > 5/5=2,23=1,38=5/2; > 7//1,2,3,16; > 1/14=-1,18=20/3(-5); > 2/9=110/2; > 6/7=2,8=2,9=2,10=2,19=2,28=1/1; > 99/9=1/99; > ------------------- > Title Card Required > ------------------- > Symbolic Z-matrix: > Charge = 1 Multiplicity = 2 > > ; > ; > ; > ; > ; > ; > Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles > Convg = 0.7166D-06 -V/T = 2.0048 > S**2 = 0.7500 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7500, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. > Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. > File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1 From owner-chemistry@ccl.net Fri May 11 16:52:00 2007 From: "Shobe, David David.Shobe_+_sud-chemie.com" To: CCL Subject: CCL:G: Vertical IP for triplet Message-Id: <-34246-070511154947-2217-dM4iTA5dbqBcVX4wTpkeeQ . server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 11 May 2007 21:49:17 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe(-)sud-chemie.com] I don't have a reference, but it should be just like calculating vertical IP for a singlet: 1. Optimize the geometry of the triplet state. In Gaussian this is done simply by using "0 3" instead of "0 1" just before the Z-matrix. 2. Do a single-point calculation at that geometry but with one fewer electron. In Gaussian this means specifying "geom=check" in the command line and replacing the "0 3" by "1 2", which means a charge of +1 and a spin multiplicity of 2. (If the cation is a quartet, change the 2 to a 4). --David Shobe -----Original Message----- > From: owner-chemistry*o*ccl.net [mailto:owner-chemistry*o*ccl.net] Sent: Thursday, May 10, 2007 9:05 PM To: Shobe, David Subject: CCL: Vertical IP for triplet Sent to CCL by: "Venkataramanan NS" [venkataramananns:+:gmail.com] Dear CCL users, Do any one have idea, how to calculate the vertical IPs for the triplet systems. If "Yes" explain and please provide me with a reference. Thanks in advance Venkataramananhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri May 11 17:26:01 2007 From: "Shobe, David David.Shobe---sud-chemie.com" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34247-070511153954-1128-jhJc+tC82OEBIUhHGhY2iQ=-=server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 11 May 2007 21:38:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [David.Shobe]=[sud-chemie.com] Usually I try "scf(maxcyc=999)" first, and "scf(qc)" second. There are about a dozen options to scf which can (sometimes) achieve SCF convergence when the default algorithm fails. The Gaussian manual lists them in the section describing the "scf" keyword. --David Shobe -----Original Message----- > From: owner-chemistry]~[ccl.net [mailto:owner-chemistry]~[ccl.net] Sent: Friday, May 11, 2007 9:39 AM To: Shobe, David Subject: CCL:G: DFT optimization Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] Hello? When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. Please suggest what to change and correct. Taye. Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 10-May-2007 ********************************************* %chk=dp[pmt-oxd-rohf.chk %mem=6MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ---------------------------------------- opt rob3lyp/6-31g(d) geom=connectivity ---------------------------------------- 1/14=-1,18=20,26=3,38=1,57=2/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/7=6/1; 5/5=2,38=5/2; 6/7=2,8=2,9=2,10=2,28=1/1; 7//1,2,3,16; 1/14=-1,18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; 4/5=5,7=6,16=3/1; 5/5=2,23=1,38=5/2; 7//1,2,3,16; 1/14=-1,18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,19=2,28=1/1; 99/9=1/99; ------------------- Title Card Required ------------------- Symbolic Z-matrix: Charge = 1 Multiplicity = 2 ; ; ; ; ; ; Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 >>>>>>>>>> Convergence criterion not met. SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles Convg = 0.7166D-06 -V/T = 2.0048 S**2 = 0.7500 Annihilation of the first spin contaminant: S**2 before annihilation 0.7500, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Fri May 11 18:01:00 2007 From: "james landon landonjhp.(-).cf.ac.uk" To: CCL Subject: CCL:G: DFT optimization Message-Id: <-34248-070511113335-13671-9u4y63jukxpa1sb35jZX1g(-)server.ccl.net> X-Original-From: james landon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 11 May 2007 15:49:18 +0100 MIME-Version: 1.0 Sent to CCL by: james landon [landonjhp^^cf.ac.uk] Hi The problem is that the SCF calculation has not reached convergence in the default number of cycles. The simplest fix is to increase the number of SCF cycles in the calculation, using SCF=maxcycle=N, where N is a number greater than 129 (200 might be a good start). You can go on increasing this number if you continue to get the same error message, but it would suggest the starting geometry is not very good, and it might be worth redrawing the compound so that it makes better chemical sense to start with (this may also decrease the number of optimization steps required, and possibly help to avoid high-energy local minima on the potential energy surface). James Landon Taye Beyene Demisse sene3095_._yahoo.com wrote: > Sent to CCL by: "Taye Beyene Demisse" [sene3095+/-yahoo.com] > Hello? > When I am optimizing a compound with DFT/B3LYP/6-31G* Gaussian reports the following message. > Please suggest what to change and correct. > > Taye. > > > Gaussian 03: x86-Win32-G03RevB.01 3-Mar-2003 > 10-May-2007 > ********************************************* > %chk=dp[pmt-oxd-rohf.chk > %mem=6MW > %nproc=1 > Will use up to 1 processors via shared memory. > Default route: MaxDisk=2000MB > ---------------------------------------- > opt rob3lyp/6-31g(d) geom=connectivity > ---------------------------------------- > 1/14=-1,18=20,26=3,38=1,57=2/1,3; > 2/9=110,17=6,18=5,40=1/2; > 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4/7=6/1; > 5/5=2,38=5/2; > 6/7=2,8=2,9=2,10=2,28=1/1; > 7//1,2,3,16; > 1/14=-1,18=20/3(1); > 99//99; > 2/9=110/2; > 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1,74=-5/1,2,3; > 4/5=5,7=6,16=3/1; > 5/5=2,23=1,38=5/2; > 7//1,2,3,16; > 1/14=-1,18=20/3(-5); > 2/9=110/2; > 6/7=2,8=2,9=2,10=2,19=2,28=1/1; > 99/9=1/99; > ------------------- > Title Card Required > ------------------- > Symbolic Z-matrix: > Charge = 1 Multiplicity = 2 > > ; > ; > ; > ; > ; > ; > Matrix for removal 18 Erem= -1656.29014707602 Crem= 0.000D+00 > >>>>>>>>>> Convergence criterion not met. > SCF Done: E(ROB+HF-LYP) = -1656.29012458 A.U. after 129 cycles > Convg = 0.7166D-06 -V/T = 2.0048 > S**2 = 0.7500 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7500, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in C:\G03W\l502.exe at Thu May 10 17:01:34 2007. > Job cpu time: 0 days 2 hours 4 minutes 45.0 seconds. > File lengths (MBytes): RWF= 59 Int= 0 D2E= 0 Chk= 2 Scr= 1> > > > > From owner-chemistry@ccl.net Fri May 11 18:36:00 2007 From: "Steve Bowlus chezbowlus . comcast.net" To: CCL Subject: CCL: chem3D et ammonium Message-Id: <-34249-070511112201-7526-M4AHrSdxgMvcRhYtj2BaMw!^!server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 11 May 2007 07:46:20 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus+/-comcast.net] I can't speak to MM2, but for MOPAC, it is most likely that the METAL involved is not parameterized. Mopac 7 does tetramethylammonium ion with no problem. Older, public versions of Mopac did not have complete parameter sets for metals with either AM1 or PM3 hamiltonians. Most particularly, transition metals were covered poorly or not at all. So I would check documentation whether the metal is covered in your version. You might also check the most recent, public (open) Mopac version to see whether the parameter sets have been expanded. Look up www.openmopac.net for information. Cheers, Steve > Bonjour > J'utilise Chem3D pour modéliser un complexe comportant un atome d'azote > secondaire ou tertiaire chélaté à un métal, donc ayant un azote de type > amonium. > Le programme Chem 3D refuse de prendre en compte cet azote faute de > définition. > Le programme répond :there are no atom types defined for this nitrogen. > > Avez vous une solution à ce problème ? > merci > cordialement > G. Miquel