From owner-chemistry@ccl.net Wed Apr 26 01:50:01 2006 From: "Goedele Roos groos]_[vub.ac.be" To: CCL Subject: CCL: tryptophane and PCM solvation model Message-Id: <-31598-060426014322-27915-fwbd616JxCCIVBSj8pwLhQ(0)server.ccl.net> X-Original-From: Goedele Roos Date: Wed, 26 Apr 2006 07:43:15 +0200 (CEST) Sent to CCL by: Goedele Roos [groos*o*vub.ac.be] Dear list, Who has some experience with tryptophane and the PCM solvation model ? I mean: is PCM also a good model for aromatic rings? Thank you in advance for help, best regards, Goedele Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17 From owner-chemistry@ccl.net Wed Apr 26 11:24:00 2006 From: "Melanie Trusselle mt237(!)bath.ac.uk" To: CCL Subject: CCL:G: Gaussian problems Message-Id: <-31599-060426084519-22657-FghTnz87uRThZEpb/aHNEA/a\server.ccl.net> X-Original-From: "Melanie Trusselle" Date: Wed, 26 Apr 2006 08:45:17 -0400 Sent to CCL by: "Melanie Trusselle" [mt237]|[bath.ac.uk] Dear All, I am a new user of Gaussian and have encountered two problems that I have been unable to resolve. The first problem is the calculation of the energy barrier between two conformers. I am using QST2 for this and my input is below. %chk=QST2.chk %mem=500MB %nproc=1 pm3 Opt=QST2 find barrier for chair-boat interconversion 1 1 zmatrix of first structure 1 1 zmatrix of second structure This input gives the error message shown below: Symbolic Z-matrix: End of file in GetChg. Error termination via Lnk1e in /usr/local/g03/l101.exe at Tue Apr 25 14:53:45 2006. Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1 I believe it relates to a lack of memory so I have tried changing %mem and have specifed extra memory when submitting the job but this has not solved the problem. I an aware that this question has been asked previously, and appologies for asking it again but there is no answer available. I am also interested in obtaining the J coupling constants for a molecule. I have used the following commands: nmr=SpinSpin b3lyp/6-31g(d) geom=connectivity An section of the output is: Total nuclear spin-spin coupling J (Hz): 1 2 3 4 5 1 0.000000D+00 2 0.482568D+02 0.000000D+00 3 0.581831D+02 0.557526D+01 0.000000D+00 4 0.167946D+03 -0.143914D+00 -0.160153D+01 0.000000D+00 5 0.107532D+01 0.576884D+02 -0.428170D+00 0.621590D+01 0.000000D+00 This is different from what I was expecting and I do not know how to relate it to my NMR specra or even if I have given the correct input. If anyone can advise me on these matters I would be most grateful. Thank you in advance. Melanie Trusselle mt237 a bath.ac.uk University of Bath, UK From owner-chemistry@ccl.net Wed Apr 26 14:01:00 2006 From: "Jozsef Csontos jozsefcsontos(_)creighton.edu" To: CCL Subject: CCL:G: Gaussian problems Message-Id: <-31600-060426120003-12690-eXeb3Gw0lzi/L5RyWD4DFw(~)server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Wed, 26 Apr 2006 10:59:28 -0500 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos+*+creighton.edu] Hi, in the first case, the first 1 means charge and the second one means multiplicity, so your conformations are charged? If not, that's the problem. On Wed, 2006-04-26 at 11:26 -0400, Melanie Trusselle mt237(!)bath.ac.uk wrote: > Sent to CCL by: "Melanie Trusselle" [mt237]|[bath.ac.uk] > Dear All, > I am a new user of Gaussian and have encountered two problems that I have been unable to resolve. The first problem is the calculation of the energy barrier between two conformers. I am using QST2 for this and my input is below. > > %chk=QST2.chk > %mem=500MB > %nproc=1 > pm3 Opt=QST2 > > find barrier for chair-boat interconversion > 1 1 > zmatrix of first structure > > 1 1 > zmatrix of second structure > > This input gives the error message shown below: > > Symbolic Z-matrix: > End of file in GetChg. > Error termination via Lnk1e in /usr/local/g03/l101.exe at Tue Apr 25 14:53:45 2006. > Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. > File lengths (MBytes): RWF= 7 Int= 0 D2E= 0 Chk= 1 Scr= 1 > > I believe it relates to a lack of memory so I have tried changing %mem and have specifed extra memory when submitting the job but this has not solved the problem. I an aware that this question has been asked previously, and appologies for asking it again but there is no answer available. > > I am also interested in obtaining the J coupling constants for a molecule. I have used the following commands: > > nmr=SpinSpin b3lyp/6-31g(d) geom=connectivity > > An section of the output is: > > Total nuclear spin-spin coupling J (Hz): > 1 2 3 4 5 > 1 0.000000D+00 > 2 0.482568D+02 0.000000D+00 > 3 0.581831D+02 0.557526D+01 0.000000D+00 > 4 0.167946D+03 -0.143914D+00 -0.160153D+01 0.000000D+00 > 5 0.107532D+01 0.576884D+02 -0.428170D+00 0.621590D+01 0.000000D+00 > > > This is different from what I was expecting and I do not know how to relate it to my NMR specra or even if I have given the correct input. > If anyone can advise me on these matters I would be most grateful. > Thank you in advance. > > Melanie Trusselle > mt237#,#bath.ac.uk > University of Bath, UK> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Wed Apr 26 18:56:00 2006 From: "Eric Hu eric.y.hu#%#gmail.com" To: CCL Subject: CCL: se and br vdw radii in g03 Message-Id: <-31601-060426185459-1569-7gF1RwK0KjnGfBLGYDePHQ]-[server.ccl.net> X-Original-From: "Eric Hu" Date: Wed, 26 Apr 2006 18:54:58 -0400 Sent to CCL by: "Eric Hu" [eric.y.hu],[gmail.com] Hi I wonder if anyone has experience with compounds having selenium and bromine atoms using B3LYP. I would like to know the radii for them to be included for charge calculations with pop=(chelpg,readradii). Thanks. Eric From owner-chemistry@ccl.net Wed Apr 26 20:20:00 2006 From: "neeraj misra misraneeraj^gmail.com" To: CCL Subject: CCL: calculation of polarizability of a molecule Message-Id: <-31602-060426201908-5266-oKVz50rHkQRry6MDf1ml2g*server.ccl.net> X-Original-From: "neeraj misra" Date: Wed, 26 Apr 2006 20:19:06 -0400 Sent to CCL by: "neeraj misra" [misraneeraj|,|gmail.com] CAN ANYONE TELL ME HOW TO CALCULATE THE POLARIZABILITY OF A MOLECULE OF 40 ATOMS. From owner-chemistry@ccl.net Wed Apr 26 22:39:01 2006 From: "Jim Kress ccl_nospam*kressworks.com" To: CCL Subject: CCL: calculation of polarizability of a molecule Message-Id: <-31603-060426214211-11961-cGbIPN0cq95G2Cwmn1xU4A/a\server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 26 Apr 2006 21:41:57 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam/./kressworks.com] 1) Don't SHOUT! 2) Use GAMESS or PCGAMESS 3) Read the user's manual 4) Use $FFCALC Or 5) Use the keywords for polarizability under $LOCAL Jim > -----Original Message----- > From: neeraj misra misraneeraj^gmail.com > [mailto:owner-chemistry_+_ccl.net] > Sent: Wednesday, April 26, 2006 8:20 PM > To: Kress, Jim > Subject: CCL: calculation of polarizability of a molecule > > Sent to CCL by: "neeraj misra" [misraneeraj|,|gmail.com] CAN > ANYONE TELL ME HOW TO CALCULATE THE POLARIZABILITY OF A > MOLECULE OF 40 ATOMS. > > > > -= 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 look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Wed Apr 26 23:14:01 2006 From: "Raji Raji raji*anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: Software for melting point analysis of DNA duplex Message-Id: <-31604-060426225841-8274-6iwh+f173ZkDPSgDAFHvvQ~~server.ccl.net> X-Original-From: "Raji Raji" Date: Wed, 26 Apr 2006 22:58:39 -0400 Sent to CCL by: "Raji Raji" [raji%a%anal.chem.tohoku.ac.jp] Dear CCL members, Can any one tell me a best and freely available (academic purpose)software which can calculate the melting point of DNA duplex alone/DNA duplex with drug molecule/DNA duplex with some common lession like AP site(s). Also, it must allow me to load the .pdb/.mol2/.xyz files of the DNA duplex and drug molecule. MeltDNA (from Abhishek Tiwari et al.)works well for simple DNA duplex with and without mismatch. But it seems, this software doesn't provide an option to upload the DNA duplex files and no way to include drugs and AP site(s). Thank you very much in advance. Best Regards, Raji.