From owner-chemistry@ccl.net Thu Sep 18 08:17:00 2008 From: "Siamkhanthang Neihsial sktn06-.-gmail.com" To: CCL Subject: CCL: UFF opt error messages Message-Id: <-37769-080918081332-6787-DoaHEffzPwSKE6uS41m7qA###server.ccl.net> X-Original-From: "Siamkhanthang Neihsial" Date: Thu, 18 Sep 2008 08:13:28 -0400 Sent to CCL by: "Siamkhanthang Neihsial" [sktn06!^!gmail.com] Dear cclers, I was working on a novel maromolecules(153 atoms,beta-allopyranose being the sugars,four of them. Four novel bases bonded by three h-bonding each, i.e two base pairs in total) which would mimics the the natural DNA in its structure. UFF forcefild (Molecular Mechanics methods in Gausssian 03)was used. . Energy calculation terminated normally. The problem was with the optimisation. The key word being #p uff opt=z-matrix geom=connectivity.It ended in error termination after step no.331 out of a maximum of 460, after 2hrs 20 mins 11.4 secs, the error messages which i got reads " Bond length on z-matrix card no. 2 is positive Bond length on z-matrix card no. 3 is positive Bond length on z-matrix card no. 4 is positive Bond length on z-matrix card no. 5 is positive Bond length on z-matrix card no. 6 is positive ................................. so on Bond length on z-matrix card no. 153 is positive But actually, in my input z-matrix, all those bondlength are all positive ! I will appreciate any help and clarification on these problems, Thanks Siamkhanthang Neihsial PhD Research Scholar Deppt.of Chemistry NEHU Campus, Shillong, India sktn06%%gmail.com From owner-chemistry@ccl.net Thu Sep 18 09:10:00 2008 From: "Karin Wichmann wichmann|-|cosmologic.de" To: CCL Subject: CCL: COSMOtherm / COSMO-RS Training Message-Id: <-37770-080916130408-28994-sF/Z4oayBIqknzUNeK1vzg*server.ccl.net> X-Original-From: Karin Wichmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 16 Sep 2008 10:08:37 +0200 MIME-Version: 1.0 Sent to CCL by: Karin Wichmann [wichmann||cosmologic.de] COSMOlogic has a small number of seats available for a free COSMOtherm training on September 29. The training is a one-day course covering COSMO-RS theory for fluid thermodynamics and its applications in the areas of chemical engineering and life science. The course will take place at our location in Leverkusen (Germany). For further information please contact us at cosmotherm (AT) cosmologic.de -- ------------------------ Dr. Karin Wichmann COSMOlogic GmbH & Co. KG Burscheider Str. 515 D-51381 Leverkusen Germany Phone +49-2171-73168-3 Fax +49-2171-73168-9 ------------------------ From owner-chemistry@ccl.net Thu Sep 18 09:56:01 2008 From: "Jozsef Csontos jcsontos.lists+/-gmail.com" To: CCL Subject: CCL: extrapolation to CBS limit Message-Id: <-37771-080917130958-14973-o80D67vVBtiLxWnyey+vTg],[server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Wed, 17 Sep 2008 11:10:56 +0200 MIME-Version: 1.0 Sent to CCL by: Jozsef Csontos [jcsontos.lists_+_gmail.com] Hi, you have 4 non-linear equations (I suppose X in the equation is equal n (2,3,4,5) in the basis set) with 3 unknown parameters (E(CBS), B and C), which means you should do non-linear regression analysis to determine the best values for the unknown parameters in your equations. (There are a couple of statistical and/or model fitting programs which are capable of doing such a thing. For example xmgrace, labplot, matematica, etc.) However, there are more to say here. Double zeta basis sets are usually not recommended for CBS fitting. It is generally advised to determine the HF and correlation energy CBS limits from different models. You can use an exponential fit for the HF part and an X^-3 fit for the correlation energy (You can even fit the same spin and the opposite spin parts using different models. For example in Jan M.L. Martins' and Antonio J.C. Varandas' works) These models are theoretically (more or less) justified. There are (semi)-empirical models as well, which were trained on databases (look for Don Truhlar's works on this topic) or models which use truncated basis sets to decrease the calculation time (Angela Wilson's and Kalju Kahn's works) Obviously, there are several other groups and people who have made important contributions to this topic. Anyway, the '97 J. Phys. Chem. paper of Helgaker and associates (106, 9639) is a good starting point for pursuing this kind of research. I hope it helps, Jozsef Sujata Guha sguha[]tnstate.edu wrote: > Sent to CCL by: "Sujata Guha" [sguha-*-tnstate.edu] > I have performed energy computations for a molecule at the CCSD(T)/cc-pVnZ (where n=D,T,Q,5)and CCSD(T)/aug-cc-pVnZ (where n=D,T,Q,5) theory levels. I'm trying to extrapolate the energies to the CBS limit for n=2-5 and am not sure of the exact procedure. I'm trying to use the equation E(X) = E(CBS) + Bexp-(X-1) + Cexp-(X-1)2. What values of B and C should I use and how would I get an energy value for n=2-5? Sorry if the question sounds basic - it is my first time to try this method of extrapolation. Any information will be much appreciated. Thank you.> > > > From owner-chemistry@ccl.net Thu Sep 18 10:20:00 2008 From: "Roy Jensen rjensen : consol.ca" To: CCL Subject: CCL:G: CASSCF on atoms... Message-Id: <-37772-080918094114-21285-MPAhSLEouPjNNFECenVanA-x-server.ccl.net> X-Original-From: "Roy Jensen" Date: Thu, 18 Sep 2008 09:41:10 -0400 Sent to CCL by: "Roy Jensen" [rjensen~!~consol.ca] Its been a while since I delved into computational work and would appreciate some assistance with a very simple calculation. My focus is now education and my project is to prepare computationally validated figure showing the ns - np energy level spacing for n = 2, 3, 4, ... Using a single configuration method, the alpha and beta s, px, py, and pz orbitals have different energies depending on their occupation. This is incorrect. The s and (px, py, pz) orbital energies must be the same and because of symmetry. That said, I would appreciate assistance setting up a simple CASSCF in Gaussian98 that outputs the orbital energies. A NBO population analysis did this for single configurations, but not for CASSCF(?) Below is the trial input file I am using for a few atoms. I want the active space to be, in the examples below, the valence p electrons in the p subshell ****************************************************************** %chk=junk.chk #P CASSCF(1,6)/3-21G pop(NBOread) Optimized geometry for atoms to determine the ns-np spacing: boron. 0 2 B $NBO RESONANCE NLMO NRT DIPOLE $end --Link1-- %chk=junk.chk #P CASSCF(2,6)/3-21G pop(NBOread) Optimized geometry for atoms to determine the ns-np spacing: carbon. 0 3 C $NBO RESONANCE NLMO NRT DIPOLE $end --Link1-- %chk=junk.chk #P CASSCF(3,6)/3-21G pop(NBOread) Optimized geometry for atoms to determine the ns-np spacing: nitrogen. 0 4 N $NBO RESONANCE NLMO NRT DIPOLE $end ****************************************************************** Your assistance in configuring the input line to produce the orbital energies would be greatly appreciated. Thanks, Dr. Roy Jensen (==========)----------------------------------------- Chemistry, Grant MacEwan College VP Professional Affairs, MacEwan Faculty Association Room 5-172J, 10700-104 Avenue Edmonton, AB T5J 4S2 780.633.3915 From owner-chemistry@ccl.net Thu Sep 18 16:39:02 2008 From: "Scott Brozell srb=osc.edu" To: CCL Subject: CCL: positive scores with amberdock Message-Id: <-37773-080918163655-1934-78Oaq1Brrno49z4xyhxwuA#%#server.ccl.net> X-Original-From: Scott Brozell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Thu, 18 Sep 2008 16:36:45 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Scott Brozell [srb(!)osc.edu] Hi, Just to follow up: This seems to have been caused by the use of PDB water coordinates that produced highly strained TIP3P waters. See this thread for more details and suggested corrections: http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-September/001716.html Scott Brozell, Ph.D. http://dock.compbio.ucsf.edu/DOCK_6/index.htm On Tue, 16 Sep 2008, Anuradha Mittal anuradha.mittal,+,gmail.com wrote: > I am carrying out amberdock recoring calculations on a set of ligands. There > are 2 waters in my system, out of which one is in the ligand binding site. > > I am getting positive amber score for all the ligands. However if I remove > the water molecules all scores are negative. > > Below are the amber scores with and without water just to give an idea: > > Keeping both waters: 38.566 > Keeping active site water: 40.36 > Keeping non active site water: 39.66 > No waters: -29.2 > > There is not much change in receptor energy in all the cases. But complex > energy varies a lot. > > Any suggestions will be much appreciated. From owner-chemistry@ccl.net Thu Sep 18 19:48:01 2008 From: "sumit mukherjee sooomitin . hotmail.com" To: CCL Subject: CCL:G: MP2 is crashing Message-Id: <-37774-080918193634-20444-l3qT1mT3l0zAqT4B8+J9Pw:-:server.ccl.net> X-Original-From: "sumit mukherjee" Date: Thu, 18 Sep 2008 19:36:31 -0400 Sent to CCL by: "sumit mukherjee" [sooomitin-,-hotmail.com] dear all, for MP2 calculation, i am using the following commands: %chk=C:\Sumit\HF-MP2\00010_HF_MP2.chk %mem=27MW # MP2(FC)/6-31G(d) Opt Freq Geom=AllCheck Guess=Read file00010_MP2(FC) 0 1 the output file is as follows (the end part): dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 66048 FType=2 FMxFil=10000 Number 0 Base 20480 End 66048 End1 66048 Wr Pntr 20480 Rd Pntr 20480 Length 45568 Error termination in NtrErr: NtrErr called from FIOCnC. .rwf file in "Scratch" folder was showing a size of 18.0 GB when Gaussian crashed!!! i am using AMD Athlon 64 processor 4000+ 2.41 GHz with 3.5 GB of RAM. is there anyway i can make this calculation successful? please help! thank you. From owner-chemistry@ccl.net Thu Sep 18 20:23:01 2008 From: "Alexander A. Bagatur yants sasha . photonics.ru" To: CCL Subject: CCL: Atomistix? Message-Id: <-37775-080918174536-3125-N0hdDhGilJ/+MtzPCn8uFw+/-server.ccl.net> X-Original-From: "Alexander A. Bagatur yants" Date: Thu, 18 Sep 2008 17:45:33 -0400 Sent to CCL by: "Alexander A. Bagatur yants" [sasha^^photonics.ru] Sorry, guys, As far as I know, the company has become bankrupt. Try to reach developers personally. Best regards Alexander Prof. Alexander A. Bagatur'yants Photochemistry Center Russian Academy of Sciences ul. Novatorov 7a Moscow 119421 Russia Phone: +7(495)9362588 Mobile: +7(916)5317022 Fax: +7(495)9361255 e-mail: sasha~~photonics.ru bagaturyants~~gmail.com > -----Original Message----- > From: owner-chemistry~~ccl.net [mailto:owner-chemistry~~ccl.net] > Sent: Thursday, September 18, 2008 12:02 AM > To: Bagaturyants, Alexander A. > Subject: CCL: Atomistix? > > > Sent to CCL by: "Susan R. Atlas" [susie.:.sapphire.phys.unm.edu] Hi, > > We have been using the commercial Atomistix atk and vnl codes > (based on SIESTA and TRANSIESTA) for the past six months to calculate > quantum transport properties (using a NEGF technique in DFT) for > nanoscale (molecular electronic) applications, and the company website > (atomistix.com) seems to have gone offline suddenly. Emails and phone > calls are going unanswered. It has been over two weeks now, and that > is longer than can be accounted for by a website crash, e.g. Google > does not turn up any news about the company. > > Does anyone on this list have any knowledge of what is going on? > If they are out of business suddenly, this will present a major > research block for us and we would need to quickly find another code > (commercial or freely available) with similar capabilities; any > recommendations would be most appreciated. > > Thanks, > > Susan > > -- > > ------------------------------------------------------------------ > Susan R. Atlas > Research Associate Professor, Physics and Astronomy Director, Cancer > Research and Treatment Center Shared Resource for > Bioinformatics and Computational Biology > > Department of Physics & Astronomy > MSC07 4220 p: 505.277.1509 > 1 University of New Mexico e: susie(-)sapphire.phys.unm.edu > Albuquerque, NM 87131-0001 n: www.phys.unm.edu/CompMaterials