From owner-chemistry@ccl.net Sun Mar 5 00:05:00 2006 From: "Elizete Ventura do Monte elizete=-=quimica.ufpb.br" To: CCL Subject: CCL:G: rasscf in gaussian Message-Id: <-31113-060304214013-16040-ii+tHa2knB4WMSV54aO/WA\a/server.ccl.net> X-Original-From: "Elizete Ventura do Monte" Date: Sat, 4 Mar 2006 21:40:11 -0500 Sent to CCL by: "Elizete Ventura do Monte" [elizete_+_quimica.ufpb.br] Dear CCLers, I am having a problem to print the configurations in a rasscf calculation with g03. When the number of CSFs is small it shows the CSFs with no problem. However, when the number is a bit larger (in my case of about 1500), it does not show any CSF. I have tried iop(4/43=2), but it didn't work. The calculation stops after the program tries to print the CSFs. The input is %mem=900Mb %chk=cas P cas(16,14,stateaverage,nroot=3,RASSCF(2,8,0,0))/6-31+g* guess=(read,alter) gfinput iop(6/7=3,4/43=2) pop=naturalorbitals maxdisk=105Gb density=current The error message is dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 65536 FType=2 FMxFil=10000 Number 0 Base 20480 End 65536 End1 65536 Wr Pntr 20480 Rd Pntr 20480 Length 45056 Error termination in NtrErr: NtrErr Called from FileIO. Does anybody can help? Thanks in advance, Elizete Ventura From owner-chemistry@ccl.net Sun Mar 5 00:40:00 2006 From: "Deepangi Pandit Deepangi.Pandit[a]gmail.com" To: CCL Subject: CCL: Transmembrane Proteins - Docking Message-Id: <-31114-060304173956-7900-A43uUxcmGxbtseM5yHeKIg{}server.ccl.net> X-Original-From: "Deepangi Pandit" Date: Sat, 4 Mar 2006 17:39:56 -0500 Sent to CCL by: "Deepangi Pandit" [Deepangi.Pandit|gmail.com] Hello: I would like to know from the community which docking programs are appropriate for performing docking experiments on transmembrane proteins like Serotonin transporter protein (SERT), Dopamine transporter protein (DAT) or GPCRs. I would also appreciate an input on scoring functions. Thanks, Deepangi From owner-chemistry@ccl.net Sun Mar 5 01:15:00 2006 From: "Changyong Qin changyong%a%wsu.edu" To: CCL Subject: CCL: GAMESS input file for CASSCF excited state calculations Message-Id: <-31115-060303132104-28446-DxZFqckD49YXgw/EqB91gQ(_)server.ccl.net> X-Original-From: "Changyong Qin" Date: Fri, 3 Mar 2006 13:21:03 -0500 Sent to CCL by: "Changyong Qin" [changyong/a\wsu.edu] Dear All, I got trouble in preparing a GAMESS input file for a CASSCF excited state calculations. First I optimized the geometry at CASSCF ground state, now I am planning to use the optimized geometry and molecular coefficients to calculated the excited state energy. If you would have experience and would like to share it with me, I would appreciate it. Thanks. Changyong Qin ground state optimization input file head CONTRL SCFTYP=MCSCF MULT=1 RUNTYP=OPTIMIZE EXETYP=RUN COORD=UNIQUE END SYSTEM MEMORY=80000000 MEMDDI=150 TIMLIM=40320 END BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 END GUESS GUESS=MOREAD NORB=55 END SCF DIRSCF=.True. DIIS=.False. END DET GROUP=C1 NCORE=41 NACT=14 NELS=14 SZ=0 END DRT NMCC=41 NDOC=7 NVAL=7 GROUP=C1 FORS=.True. END MCSCF MAXIT=400 SOSCF=.False. FULLNR=.True. CISTEP=GUGA END STATPT NSTEP=100 END DATA Dihydrobenzvalene Transition State Geometry Optimization C1 1 6.0 0.0670338516 1.6109629599 0.7533357984 2 6.0 -0.0670339148 -1.6109628824 0.7533357759 ... END VEC ... END excited state energy input file head (I tried, but not succeeded) CONTRL SCFTYP=MCSCF MULT=1 RUNTYP=ENERGY EXETYP=RUN COORD=CART NOSYM=1 END SYSTEM MEMORY=80000000 MEMDDI=150 TIMLIM=40320 END BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 END GUESS GUESS=MOREAD NORB=234 END SCF DIRSCF=.True. DIIS=.False. END DET GROUP=C2 NCORE=41 NACT=14 NELS=14 SZ=0 ISTSYM=2 END GUGDIA NSTATE=2 END GUGDM2 WSTATE(1)=0,1 IROOT(1)=2,1 END DRT NMCC=41 NDOC=7 NVAL=7 GROUP=C2 FORS=.True. END MCSCF MAXIT=400 SOSCF=.False. FULLNR=.True. CISTEP=GUGA END STATPT NSTEP=100 END DATA Dihydrobenzvalene Transition State Geometry Optimization Cn 2 1 6.0 0.0655686117 1.6135370382 0.7544000004 .. END VEC ...(optimized ground state MC) END From owner-chemistry@ccl.net Sun Mar 5 01:50:00 2006 From: "zborowsk^_^chemia.uj.edu.pl" To: CCL Subject: CCL: Phonon Spectra of Organic Molecular Crystals Message-Id: <-31116-060303085935-15041-lWH5YcGkJhbc1LcamlUB4A[]server.ccl.net> X-Original-From: zborowsk!A!chemia.uj.edu.pl Date: Fri, 3 Mar 2006 14:59:10 +0100 (CET) Sent to CCL by: zborowsk===chemia.uj.edu.pl Hi Sigifredo I am not familiar with such calculations but maybe this help http://wolf.ifj.edu.pl/phonon/ Regards > Sent to CCL by: "Roel Sigifredo Sanchez-Carrera" [roel _ gatech.edu] > Dear CCL members, > > I would like to know if there is any computational software (commercial or > non-commercial) that will allow me to compute the phonon spectra of > organic molecular crystals at either semiempirical, ab initio or DFT > level. > > In advance thanks for your response. > > Sigifredo Sanchez-Carrera > roel-$-gatech.edu > Georgia Institute of Technology > 770 State Street > Atlanta, GA 30332-0400 -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk.:.chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Sun Mar 5 02:30:00 2006 From: "Robinson, James James.Robinson()evotec.com" To: CCL Subject: CCL: force calculation on mopac Message-Id: <-31117-060304210915-12400-IvxeRX2QB0zTrKllGqyAwg.:.server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 5 Mar 2006 01:24:10 -0000 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson**evotec.com] Add the keyword LET DDMIN=0.00 GEO-OK PRECISE. This sould work, if that fails then try the SIGMA optimisation instead of EF/TS. As for calculating frequency with FORCE, add THERMO keyword and LET DDMIN=0.00 GEO-OK. You might have to use the geometry/wavefunction in the .RES file or make sure you use the geometry in the .ARC file. Dr J Robinson, UK. -----Original Message----- > From: owner-chemistry#%#ccl.net [mailto:owner-chemistry#%#ccl.net] Sent: 04 March 2006 23:03 To: Robinson, James Subject: CCL: force calculation on mopac Sent to CCL by: "Gon alo Justino" [goncalo.justino*zmail.pt] Dear all, I recently upgraded to mopac 2002 built in ChemDraw for Windows. I'm trying to get a force calculation running but I'm stuck at this: - when I use AM1 GNORM=0.01 everything is ok, i get a nice output file; - when I use AM1 FORCE I get back ** GRADIENT IS TOO LARGE TO ALLOW FORCE MATRIX TO BE CALCULATED, (LIMIT=10) ** EITHER ADD 'LET' OR REDUCE GRADIENT USING 'TS' OR OTHER GEOMETRY OPTIMIZER~ - if I use AM1 FORCE TS, or AM1 FORCE LBFGS, I get back MORE THAN ONE GEOMETRY OPTION HAS BEEN SPECIFIED; CONFLICT MUST BE RESOLVED BEFORE JOB WILL RUN. This happens for any molecule. Is this my incompetence, software conflict or simple mis-installation? Any suggestion is welcome, Gonalo Justino goncalo.justino[a]zmail.pthttp://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 Sun Mar 5 22:01:00 2006 From: "Raji Raji raji#anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: Molekel Message-Id: <-31118-060305220021-858-WP29zbg7pUH/vTYl1lkD1g-.-server.ccl.net> X-Original-From: "Raji Raji" Date: Sun, 5 Mar 2006 22:00:17 -0500 Sent to CCL by: "Raji Raji" [raji{}anal.chem.tohoku.ac.jp] Dear CCL members, I can't able to download the molekel*.win32.zip and molekel-objects*.win32.zip files. So can anyone send me these zip files for windows platform. Thank you very much in advance. Regards, Raji.