From owner-chemistry@ccl.net Fri May 18 01:22:01 2012 From: "saman usmani dr.usmani09]=[gmail.com" To: CCL Subject: CCL: metal treatment in simulation Message-Id: <-46924-120517002930-18040-syM2I3ZlDGcdGmdqzELiPQ|server.ccl.net> X-Original-From: "saman usmani" Date: Thu, 17 May 2012 00:29:27 -0400 Sent to CCL by: "saman usmani" [dr.usmani09 : gmail.com] Hello, I am working with protein having two MG ions with the distance of 3.98 in the original pdb, having the backbone role in making coordination with protein and ligand upon introduction. But when I start minimizing it using Amber11 (sander), the distance between two metals increases gradually (upto 0.5). I have change the restrain force to maintain it but of no use. How can I manage this problem kindly help me. regards, Saman From owner-chemistry@ccl.net Fri May 18 01:57:00 2012 From: "upen adk upen_ccl . yahoo.com" To: CCL Subject: CCL: DFT reference Message-Id: <-46925-120517172740-30660-af2QHl5My/Co8vNXzGQpcA_+_server.ccl.net> X-Original-From: "upen adk" Date: Thu, 17 May 2012 17:27:29 -0400 Sent to CCL by: "upen adk" [upen_ccl###yahoo.com] Dear All, Can you please provide me a reference for a DFT 'Becke "Half and Half" with LYP/VWN correlation'(IOp(3/74)=-3). Thank you Upen From owner-chemistry@ccl.net Fri May 18 03:27:00 2012 From: "saman usmani dr.usmani09]*[gmail.com" To: CCL Subject: CCL: protein backbone restain Message-Id: <-46926-120518032627-12749-2vasMp3RUHLwpnQKvALTKA]![server.ccl.net> X-Original-From: "saman usmani" Date: Fri, 18 May 2012 03:26:24 -0400 Sent to CCL by: "saman usmani" [dr.usmani09:_:gmail.com] Hello, I wish to run protein simulation using sander with restrained protein backbone. Can anyone guide me, how to prepare the input file for this? From owner-chemistry@ccl.net Fri May 18 10:39:00 2012 From: "Jim Kress ccl_nospam!A!kressworks.com" To: CCL Subject: CCL:G: DFT reference Message-Id: <-46927-120518094829-24150-g8iCIXxTg7Rsgm+9z/6hTg##server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 18 May 2012 09:48:00 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam[a]kressworks.com] If you have a legal copy of Gaussian, why don't you ask them? Even a web search will reveal this: http://www.gaussian.com/g_tech/g_ur/k_dft.htm Jim Kress > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com=ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com=ccl.net] On Behalf > Of upen adk upen_ccl . yahoo.com > Sent: Thursday, May 17, 2012 5:27 PM > To: Kress, Jim > Subject: CCL: DFT reference > > > Sent to CCL by: "upen adk" [upen_ccl###yahoo.com] Dear All, Can you > please provide me a reference for a DFT 'Becke "Half and Half" with > LYP/VWN correlation'(IOp(3/74)=-3). > > Thank you > > UpenTo > 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 look up the X- > Original-From: line in the mail header.> From owner-chemistry@ccl.net Fri May 18 11:13:00 2012 From: "Lara Mart nez Fern ndez lara.martinez-$-uam.es" To: CCL Subject: CCL: Ricc2 triplet state optimization Message-Id: <-46928-120518104150-30328-gm70gv4LFC64kiIBUUnzGg[-]server.ccl.net> X-Original-From: "Lara Mart nez Fern ndez" Date: Fri, 18 May 2012 10:41:47 -0400 Sent to CCL by: "Lara Mart nez Fern ndez" [lara.martinez=-=uam.es] Dear all, We are trying to optimize the first triplet exited state of a Pt complex with cc2 using turbomole. The most important section of the input is summarized below. The optimization is not even able to make a single optimization cycle and it stops, after computing the CC2 excitation energies, with the error: Gradient & energy will be written to control file for the excited state (mult.,sym.,index,energy): 3a 1 ( 1.71 eV) The semi-canonical algorithm will be used for densities === B matrix transformation for 1 state(s) === error in gradient step (1) Has anyone come across this problem? Is it actually possible to optimize triplet excited state using ricc2 approach? Thank you very much in advance. INPUT $energy file=energy $grad file=gradient $forceapprox file=forceapprox $lock off $maxcor 2000 $denconv 0.10000000E-06 $cbas file=auxbasis $ricc2 geoopt model=cc2 state=(a{3} 1) $excitations irrep=a multiplicity=3 nexc=1 $dipole from dscf x 1.82648951788329 y -3.27090768662823 z -0.50465397033019 a.u. | dipole | = 9.6082698777 debye $freeze implicit core= 36 virt= 0 $title * $closed shells a 1-129 ( 2 ) $actual step ricc2 From owner-chemistry@ccl.net Fri May 18 11:49:00 2012 From: "uekstrom\a/gmail.com uekstrom\a/gmail.com" To: CCL Subject: CCL: Looking for 2 electron full CI "grid" code Message-Id: <-46929-120518110437-21165-4skGL+qcXTiWB/6PPj0oCw*server.ccl.net> X-Original-From: "uekstrom()gmail.com" Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 18 May 2012 17:04:30 +0200 MIME-Version: 1.0 Sent to CCL by: "uekstrom]~[gmail.com" [uekstrom]~[gmail.com] Dear all, I am looking for a code that can compute the 2 electron full CI ground state energy and density for an arbitrary (not necessarily atomic) potential in a box. Any ideas? (This is for the 3d problem, 1d I can solve easily). Regards, Ulf Ekstrom, University of Oslo From owner-chemistry@ccl.net Fri May 18 12:24:00 2012 From: "N. Sukumar nagams : rpi.edu" To: CCL Subject: CCL:G: DFT reference Message-Id: <-46930-120518114038-16136-dQzLCgldDzoBooaMiet3ug{}server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 18 May 2012 11:40:16 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams^^rpi.edu] Why bother using google when you can ask CCL? N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research Professor of Chemistry Shiv Nadar University -------------------------- "When you get exactly the opposite result to what you predict, you know it is right, because there is no bias." -- David Nutt, Imperial College, London. ==============Original message text=============== Sent to CCL by: "Jim Kress" [ccl_nospam[a]kressworks.com] If you have a legal copy of Gaussian, why don't you ask them? Even a web search will reveal this: http://www.gaussian.com/g_tech/g_ur/k_dft.htm Jim Kress > -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com*|*ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com*|*ccl.net] On Behalf > Of upen adk upen_ccl . yahoo.com > Sent: Thursday, May 17, 2012 5:27 PM > To: Kress, Jim > Subject: CCL: DFT reference > > > Sent to CCL by: "upen adk" [upen_ccl###yahoo.com] Dear All, Can you > please provide me a reference for a DFT 'Becke "Half and Half" with > LYP/VWN correlation'(IOp(3/74)=-3). > > Thank you > > UpenTo > 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 look up the X- > Original-From: line in the mail header.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Fri May 18 13:50:00 2012 From: "quartarolo ~ unical.it" To: CCL Subject: CCL: Ricc2 triplet state optimization Message-Id: <-46931-120518133801-28547-flCfLUqQnene6oN6RqQ/QA-#-server.ccl.net> X-Original-From: quartarolo..unical.it Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Fri, 18 May 2012 19:37:47 +0200 MIME-Version: 1.0 Sent to CCL by: quartarolo---unical.it Dear Lara, I made successfully a similar calculation for an organic molecule (60 atoms). Why you don't contact directly the support of Turbomole? Quartarolo Domenico > Dear all, > > We are trying to optimize the first triplet exited state of a Pt > complex with cc2 using turbomole. The > most important section of the input is summarized below. > The optimization is not even able to make a single optimization > cycle and it stops, after computing > the CC2 excitation energies, with the error: > > Gradient & energy will be written to control file > for the excited state (mult.,sym.,index,energy): > 3a 1 ( 1.71 eV) > > > The semi-canonical algorithm will be used for densities > > === B matrix transformation for 1 state(s) === > > error in gradient step (1) > > > > Has anyone come across this problem? Is it actually possible to > optimize triplet excited state using > ricc2 approach? > > Thank you very much in advance. > > > INPUT > $energy file=energy > $grad file=gradient > $forceapprox file=forceapprox > $lock off > $maxcor 2000 > $denconv 0.10000000E-06 > $cbas file=auxbasis > $ricc2 > geoopt model=cc2 state=(a{3} 1) > $excitations > irrep=a multiplicity=3 nexc=1 > $dipole from dscf > x 1.82648951788329 y -3.27090768662823 z > -0.50465397033019 a.u. > | dipole | = 9.6082698777 debye > $freeze > implicit core= 36 virt= 0 > $title > * > $closed shells > a 1-129 ( 2 ) > $actual step ricc2> > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. **** Riservatezza / Confidentiality **** In ottemperanza al D.Lgs. n. 196 del 30/6/2003 in materia di protezione dei dati personali, le informazioni contenute in questo messaggio sono strettamente riservate ed esclusivamente indirizzate al destinatario indicato (oppure alla persona responsabile di rimetterlo al destinatario). Vogliate tener presente che qualsiasi uso, riproduzione o divulgazione di questo messaggio e' vietato. Nel caso in cui aveste ricevuto questo messaggio per errore, vogliate cortesemente avvertire il mittente e distruggere il presente messaggio. From owner-chemistry@ccl.net Fri May 18 16:36:00 2012 From: "Parmar, Payal payal.parmar=wsu.edu" To: CCL Subject: CCL: TINKER - to use mixed parameters in the .key file Message-Id: <-46932-120514182252-8403-g9sKEnK9uqFRADQRa4d2bg(_)server.ccl.net> X-Original-From: "Parmar, Payal" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_FDE4DA05D1600146A158C6F05118D397341E3A1DEXMB06adwsuedu_" Date: Mon, 14 May 2012 22:22:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Parmar, Payal" [payal.parmar~~wsu.edu] --_000_FDE4DA05D1600146A158C6F05118D397341E3A1DEXMB06adwsuedu_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Tinker-experts, In the TINKER .key file, we input the unmixed Van der Waals parameters. Is there a way I could work with the mixed parameters in the TINKER? Thank You. Payal Parmar Washington State University, Pullman, WA. USA. --_000_FDE4DA05D1600146A158C6F05118D397341E3A1DEXMB06adwsuedu_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear Tinker-experts,

In the TINKER .key file, we input the unmixed Van der Waals param= eters. 
Is there a way I could work with the mixed parameters in the TINKER?

Thank You. 

Payal Parmar
Washington State Universi= ty,
Pullman, WA.
USA.
--_000_FDE4DA05D1600146A158C6F05118D397341E3A1DEXMB06adwsuedu_-- From owner-chemistry@ccl.net Fri May 18 21:06:01 2012 From: "Nguyen Minh Ly nguyenminhly2209---yahoo.com" To: CCL Subject: CCL: SN1 Transition state Message-Id: <-46933-120518004908-32072-2q6OkDNDGgVgGsaitoS4gw%x%server.ccl.net> X-Original-From: "Nguyen Minh Ly" Date: Fri, 18 May 2012 00:49:05 -0400 Sent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209:yahoo.com] Hi all, I have optimized my structure (C4H9Cl) to find SN1 transition state (The first stage). After that, I used IRC keyword to find reaction path. I think the reaction path is true Maybe my SN1 transition state is wrong because in the first state of SN1 reaction, the transition state have C in C - Cl which sp3 Carbon. But in my structure, C in C - Cl is sp2 carbon. Please help me I don't know how to do that. This is my input IRC file and I think It have no problems ! %chk=E:/SN1 hoan chinh/check.chk %mem=50MW %nproc=1 # irc=(maxpoints=200,calcfc) rhf/sto-3g* scrf=(solvent=water) nosymm geom=connectivity scf=tight Title Card Required 0 1 C C 1 B1 H 2 B2 1 A1 H 2 B3 1 A2 3 D1 H 2 B4 1 A3 3 D2 C 1 B5 2 A4 4 D3 H 6 B6 1 A5 2 D4 H 6 B7 1 A6 2 D5 H 6 B8 1 A7 2 D6 C 1 B9 2 A8 6 D7 H 10 B10 1 A9 2 D8 H 10 B11 1 A10 2 D9 H 10 B12 1 A11 2 D10 Cl 1 B13 2 A12 6 D11 B1 1.47431703 B2 1.14686182 B3 1.08428105 B4 1.08428709 B5 1.51651009 B6 1.09487367 B7 1.08671207 B8 1.08648693 B9 1.51651863 B10 1.08650334 B11 1.08670307 B12 1.09487708 B13 2.92785823 A1 94.54272741 A2 113.17487272 A3 113.17070963 A4 120.32991518 A5 105.75995343 A6 111.06039901 A7 110.61649956 A8 120.33488143 A9 110.61098280 A10 111.06799304 A11 105.75784892 A12 76.76384792 D1 114.35013589 D2 -114.34007794 D3 -154.81170384 D4 94.31903244 D5 -147.66434619 D6 -23.53114821 D7 178.28321748 D8 23.60609839 D9 147.74280879 D10 -94.23237154 D11 -90.83478191 1 2 1.0 6 1.0 10 1.0 2 4 1.0 5 1.0 3 4 5 6 7 1.0 8 1.0 9 1.0 7 8 9 10 11 1.0 12 1.0 13 1.0 11 12 13 14