From owner-chemistry@ccl.net Fri Oct 17 04:00:00 2008 From: "Jozsef Csontos jcsontos.lists**gmail.com" To: CCL Subject: CCL:G: Counterpoise Calculations in G03 Message-Id: <-37932-081017035355-29779-+JmpxllNLHhvWsPOhbZeWQ+*+server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 17 Oct 2008 09:53:32 +0200 MIME-Version: 1.0 Sent to CCL by: Jozsef Csontos [jcsontos.lists*gmail.com] Hi, if you specify the counterpoise=2 keyword in the route section gaussian's gonna calculate 5 molecular systems. Let's say you want to calculate the interaction energy between fragment A and B, then the following quantities will be calculated: E(AB, DCBS), E(A,DCBS), E(B,DCBS), E(A,MCBS), E(B,MCBS), where for instance E(AB, DCBS) means the energy of the AB dimer in the dimer centered basis set (this is System(CP) in your mail); MCBS is for the monomer centered basis set. So basically you don't need to setup any other calculations. The cp corrected interaction energy is equal to E(AB, DCBS)-E(A,DCBS)-E(B,DCBS); the MCBS calculations are for calculating the value of BSSE. I'm not sure whether the counterpoise calculation is possible with mixed basis set but it should be. Otherwise you can try to specify the ghost atoms explicitly (http://gaussian.com/g_ur/m_molspec.htm), however, this means 3 input files for the cp corrected energy. I hope it helps, Jozsef Dennis Devine sahaimic(!)gmail.com wrote: > Sent to CCL by: "Dennis Devine" [sahaimic * gmail.com] > Hi I want to do calculations on a system composed of selected receptor residues and the ligand using the Gaussian program to obtain interaction energies for each of the fragments of the system. In the end i hope to understand which fragment contributes most to the stability of the system. But i am not sure how to go about this. > > I am trying to do it by first using an energy minimized structure of the full protein obtained from MD simulations on GROMACS. Then selecting key residues and the ligand and then doing the energy calculations using Gaussian. But i am sure this is not enough and i need to compensate for BSSE using the CP method. However, i am not sure how these files can be set up. > > Ideally I want to use the locally dense basis set (LDBS) approach, where the model-system will been partitioned into two different regions, which were assigned basis sets of different accuracy. The atoms interacting directly with the ligand and the ligand itself will be described by 6-31g* basis set. While the less accurate 3-21G* basis set will be used for all remaining atoms. I plan on using the MP2 level of theory. > > Say i am looking at the interaction energy of one residue and the ligand. Do i need to set up 3 files to calculate the interaction energy using G03. Namely: > 1. With the counterpoise=2 in the route card with the fragments described - with the mixed basis set. > 2. Fragment one - energy calculation with its basis set. > 3. Fragment two - energy calculating with its basis set. > > and the calculation in the end would be > > E(int)CP = System (CP) - (F1+F2) (all in hartrees - then converted to KJ/mol) > > Any comments and suggestions in how to go about doing this would be most appreciated. > > Thank you very much in advance for the assistance. > > Best regards, > > Dennis > sahaimic ~~ gmail.com> > > > From owner-chemistry@ccl.net Fri Oct 17 05:52:01 2008 From: "Arthur computationalboy]=[gmail.com" To: CCL Subject: CCL: molecular modeling of copper (II) coordination complex Message-Id: <-37933-081017035912-30633-ToW7aZkBYRBO6a+hZLMqdQ-$-server.ccl.net> X-Original-From: Arthur Content-Type: multipart/alternative; boundary="----=_Part_28193_20323575.1224230341675" Date: Fri, 17 Oct 2008 15:59:01 +0800 MIME-Version: 1.0 Sent to CCL by: Arthur [computationalboy+*+gmail.com] ------=_Part_28193_20323575.1224230341675 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all: I have problems in modeling coordination complex such as copper (II)- His complex for conformational analysis and global lowest energy computation. Can anyone give me some instructions on how to consider the coordination bonds? I cannot construct the complex structure in Sybyl (Tripos) since the software allways considers the bonds as covalent. Any suggestion would be greatly appreciated. Yours sincerely Arthur -- Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China Tel : +86 24 23986419 Fax: +86 24 23995043 E-Mail: wjmed(at)126.com ; computationalboy(at)gmail.com ------=_Part_28193_20323575.1224230341675 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all:
I have problems in modeling coordination complex such as copper (II)- His complex for conformational analysis and global lowest energy computation.  Can anyone give me some instructions on how to consider the coordination bonds? I cannot construct the complex structure in Sybyl (Tripos) since the software allways considers the bonds as covalent.
Any suggestion would be greatly appreciated.

Yours sincerely Arthur
--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail:  wjmed(at)126.com ;
      computationalboy(at)gmail.com ------=_Part_28193_20323575.1224230341675-- From owner-chemistry@ccl.net Fri Oct 17 06:47:01 2008 From: "Martin Bohl martin a moldiscovery.com" To: CCL Subject: CCL: Molecular Discovery: Cytochrome P450 Consortium Message-Id: <-37934-081017053458-1740-5QGIKkhQf/0u6MisCydo7g++server.ccl.net> X-Original-From: "Martin Bohl" Date: Fri, 17 Oct 2008 05:34:44 -0400 Sent to CCL by: "Martin Bohl" [martin.:.moldiscovery.com] Molecular Discovery Ltd, a privately held, UK based pharmaceutical software company, today announced the launch of a Consortium aimed at solving some of the most important problems in the predictive metabolism of potential drug candidates, an area that is critical for pharmaceutical research. The Cytochrome P450 Consortium will for the first time generate comprehensive experimental data for human metabolism, allowing the development of predictive in silico models; both the data and the models will be made available to all of the Consortium members. Seven pharmaceutical companies (Accelera, AstraZeneca, Novartis, Pfizer, Sanofi-Aventis, Servier, and Solvay Pharmaceuticals) have already signed up to participate, and there is strong interest from a number of other companies. Specifically, the Consortium will produce high quality and standardised experimental data (to guarantee homogeneity of the information) for several of the most relevant human cytochromes. In silico models will then be developed to predict (i) the metabolic rate of potential substrates of selected CYP isozymes, (ii) the likelihood of chemical compounds to be a substrate of such CYP isozymes, and (iii) potential inhibitors for such CYP isozymes including classification of the CYP inhibition type, isoform selectivity, metabolic stability, sites of metabolism, and metabolic reaction pathway elucidation. Molecular Discovery already has a strong background in this area, as demonstrated by the success of its MetaSite software (for the prediction of substrates site of metabolism), and the resulting data and models will be used to enhance future versions. Those companies interested in joining the Consortium can still do so, by contacting Dr. Martin Bohl of Molecular Discovery (Tel: +49 171 174 11 61, Email: martin[at]moldiscovery[dot]com) From owner-chemistry@ccl.net Fri Oct 17 11:55:00 2008 From: "Senthil Natesan sen.natesan ~~ yahoo.com" To: CCL Subject: CCL: Problem in Qsite (Schrodinger) Calculation Message-Id: <-37935-081017114950-15744-cJ33iu7WORPfWEq0nbDjDQ _ server.ccl.net> X-Original-From: "Senthil Natesan" Date: Fri, 17 Oct 2008 11:49:46 -0400 Sent to CCL by: "Senthil Natesan" [sen.natesan * yahoo.com] I am trying to do QM/MM Calculation for protein-ligand complex using Qsite module in Schrodinger and ended up with the following error. ************************************************************************** Atomtyping finished successfully for molecule: %IMPACT-I(foldmain): finished parameter assignment PARM read from file paramstd.dat Parameter obtained from atomtyping No match for QM neighbor atom in data file 6 start of program pre ERROR: fatal error -- debug information follows There's no &zmat section in input file! ------------------------------------------------------------ Jaguar cannot recover from this error and will now abort. ***************************************************************************** I have previously run the identical calculations successfully with the same complex but different input files. I checked both set of files, but could not figure out any difference as such. The only difference is, the preparation before this step was done by sybyl version (7.1) earlier and now sybyl8.0. I would appreciate any help in this regard. Thanks for your valuable time. Senthil Natesan senthil.natesan() ndsu.edu sen.natesan() yahoo.com From owner-chemistry@ccl.net Fri Oct 17 13:24:00 2008 From: "Youzhao Lan lyzhao%zjnu.cn" To: CCL Subject: CCL:G: A problem about the CI expansion coefficients Message-Id: <-37936-081017032310-26149-CAlol30rHMYdHypZrkvSaA[]server.ccl.net> X-Original-From: "Youzhao Lan" Date: Fri, 17 Oct 2008 03:23:05 -0400 Sent to CCL by: "Youzhao Lan" [lyzhao() zjnu.cn] I calculated the first excited state of a doublet molecule using TDDFT under Gaussian03 and got the result: Excited State 1: ?Spin -BG 0.2962 eV 4185.32 nm f=0.0000 98B -> 99B 1.03006 This state for optimization and/or second-order correction. Total Energy, E(RPA) = -5114.25187004 Copying the excited state density for this state as the 1-particle RhoCI density. Excited State 2: ?Spin -BU 1.0708 eV 1157.87 nm f=0.0040 98A ->101A 0.11472 98A ->102A 0.24101 99A ->100A 0.35207 97B -> 99B 0.96071 98B ->100B 0.22098 Could anyone tell me whether it is available that the CI expansion coefficient 1.03006 is larger than 1? I have investigated the excitation properties of many systems and hardly gotten such CI expansion coefficient. Great thanks for any help!! Welcome any references. From owner-chemistry@ccl.net Fri Oct 17 13:59:01 2008 From: "Nand Ng andyng111[*]hotmail.com" To: CCL Subject: CCL: imaginary part of density matrix Message-Id: <-37937-081017131126-25008-53Dmik4UiG2HdQUATNvpOw .. server.ccl.net> X-Original-From: "Nand Ng" Date: Fri, 17 Oct 2008 13:11:23 -0400 Sent to CCL by: "Nand Ng" [andyng111|,|hotmail.com] Dear all, When solving time-dependent schrodinger equation, what is the physical meaning of the imaginary part of density matrix? Thanks all Regards, Nand From owner-chemistry@ccl.net Fri Oct 17 14:34:00 2008 From: "Keith Refson krefson-*-googlemail.com" To: CCL Subject: CCL: augmented charge density in Ultra Soft Pseodopotentials .. can someone explain ? Message-Id: <-37938-081017112825-10612-kMZMi2kRTKTkVxSSz5f/hg ~~ server.ccl.net> X-Original-From: Keith Refson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Fri, 17 Oct 2008 16:27:47 +0100 Mime-Version: 1.0 Sent to CCL by: Keith Refson [krefson-x-googlemail.com] Dear Peter, You might get a more detailed answer to this question on a specific mailing list for one of the codes which uses this technology. However if you are looking for a conceptual answer I'll have a try.  > On Thu, 2008-10-16 at 15:56 +0100, Peter Ryan ryanp- -tcd.ie wrote: > Sent to CCL by: "Peter Ryan" [ryanp|-|tcd.ie] > Hi Folks. > In reading up on the details of ulta soft pseudopotentials i have > come acros this sentance and varients of it quite a lot. > .....In order to recover the full electronic charge of the system > when using ultra soft pseudo potentials , the electron density given > by the square moduli of the wavefunctions is augmented in the core > regions. ... > > Can someone please explain what the phrase "augmented" actually > means in this context. When replacing the "all-electron" orbitals containing nodes with nodeless pseudo-wavefunctions, the "norm-conservation" condition is that \int |phi_pseudo(r)|**2 = \int |phi_AE(r)|**2. A consequence of this is that orbitals with no nodes - 1s, 2p, 3d and 4f have pseudo-orbitals which are almost as sharply peaked as the all-electron ones. Therefore a large plane-wave basis set is needed to describe them resulting in expensive computations. David Vanderbilt's ultrasoft scheme relaxes the norm-conserving condition, and allows the KS equations to be replaced by a similar set of "generalised eigenvalue" equations resulting in much softer orbitals. The correction for the un-normalised orbitals is contained in the S matrix, but the key point is that softer, un-normalised orbitals are obtained. However the charge density constructed from these orbitals is clearly disasterously wrong - it does not even integrate to the number of electrons in the system, so the Hartree and XC potentials can not be evaluated from it. So the ultrasoft scheme puts back the missing electron density quite accurately by adding augmentation charge density terms constructed using the pseudo-orbitals, and a set of additional quantities computed from the all-electron calculation, which accompany the pseudopotential. There's more to it than the above, but this is the essence. > Are we just adding back the charge that we have just removed while > implementing ultra soft pseudopotentials ? Yes. > i don't get it : ) Whats the point if the charge is just added back ... Because the *orbitals* are still less peaked and require a smaller basis set, even though the full charge density is constructed by less direct means. This only needs to happen once per SCF cycle, not once per band, so the additional expense of handling the highly-peaked charge density is not high. Hope this answers your question. Keith Refson -- Dr Keith Refson, Building R3 Rutherford Appleton Laboratory Chilton Didcot Oxfordshire OX11 0QX T: 01235 778023 Keith.Refson* F: 01235 445720 *stfc.ac.uk From owner-chemistry@ccl.net Fri Oct 17 15:09:01 2008 From: "willsd * appstate.edu" To: CCL Subject: CCL:G: Overtone anharmonicities and anharmonic frequencies from Gaussian. Message-Id: <-37939-081016182008-7681-vayRbmlatS9mjA8q/njIMQ##server.ccl.net> X-Original-From: Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 16 Oct 2008 21:37:11 GMT MIME-Version: 1.0 Sent to CCL by: [willsd.[-].appstate.edu] I'd recommend the VSCF method in GAMESS. You can specify how many quanta you want. So in a three mode system (like water, perhaps) with vibrational quantum numbers (n1, n2, n3) you can compute the vibrational energies of a variety of excitations: fundamentals:(1,0,0); (0,1,0); (0,0,1) first overtones: (2,0,0); (0,2,0); (0,0,2) second overtones: (3,0,0), (0,3,0), (0,0,3) (Differences between these and 2x or 3x the fundamentals will give you the first and second anharmonicities) combination bands: (1,1,0); (1,0,1), (0,1,1) higher combinations: (2,1,0), (1,2,0), (2,0,1), (1,0,2), (0,1,2), (0,2,1) It is possible to compute the potential with all combinations of three (not just one or two) modes, but I am not sure if you can get energies with excitations in three different modes. GAMESS can also compute dipoles at all points on the one (or one and two) mode grids it uses, so it can also estimate IR intensity for these excitations, not just the frequencies. There are a LOT of grid points for two mode calculations even for smallish (say 10 atom) molecules, and rather good energies are needed to get good frequencies, so it can be slow... a triple zeta mp2 calculation for C4H5N may take several weeks on 8 cores of a xeon based cluster. The results are really quite good though... many fundamentals, overtones, and combination bands predicted within 20 cm-1 or so of observed frequencies, with relative intensities close enough to observed intensities to be useful for assigning spectra. Steve Williams ----- Original Message ----- > From: "Roman D. Gorbunov rgorbuno+/-aecom.yu.edu" Date: Thursday, October 16, 2008 1:18 pm Subject: CCL:G: Overtone anharmonicities and anharmonic frequencies from Gaussian. To: "Williams, Steve " > > Sent to CCL by: "Roman D. Gorbunov" [rgorbuno _ aecom.yu.edu] > Dear CCL subscribers, > > I need to calculate overtone anharmonicities of vibrational modes > of a molecule. In other words I need to know (E_1 - E_0) - (E2 - > E1), where E_j are energy levels of a vibrational states. > > I have managed to get a normally terminated Gaussian calculations > of anharmonic frequencies (using Freq=(HPModes,Anharmonic)). So, in > my output file I have harmonic and anharmonic frequencies of the > normal modes. > > The problem is that I do not know how the "overtone > anharmonicities" are related with the "anharmonic frequencies". The > problem is that I do not know the definition for the anharmonic > frequencies. I can try to ges. May be "anharmonic frequency" are > defined as the transition frequency from the first excited state to > the ground state in the cubic potential? But even if it is defined > like that it still does not give a direct answer on my question > (how to get the overtone anharmonicites). > > Can anybody help me with that? > > Thank you in advance. > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the [-] sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > From owner-chemistry@ccl.net Fri Oct 17 15:43:01 2008 From: "Curt M. Breneman brenec:-:rpi.edu" To: CCL Subject: CCL: October 20th (Monday) Final Deadline Reminder: Invitation to submit to "Nanomaterials Modeling and Informatics" at ACS Salt Lake City Message-Id: <-37940-081017144941-24706-TB9V2vmzotPa2UZSNkMVPA[*]server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 17 Oct 2008 14:49:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec ~ rpi.edu] Dear Colleagues, The new "Nanomaterials Modeling and Informatics" symposium within COMP Division program of the ACS National Meeting in Salt Lake City, UT March 22 29, 2009 is open for submissions through the ACS OASys system. If you are modeling nanotubes or related nanoparticulates, we'd like to hear from you! Note: All abstracts must be entered no later than Monday, October 20th. Nanotube and nanomaterials modeling is a new program area for the COMP Division, but it is an emerging area and directly aligned with the "Nanoscience" theme of this ACS meeting. This is a rapidly developing field, so we at COMP are providing a venue for people to present their latest developmental work in this area. This announcement is deliberately broad because we envision the symposium to be rich in diverse methodologies and preliminary results, and will include discussions of current "Best" practices in all aspects of the computational modeling of nanotubes and nanocomposite materials. Sincerely, Curt Breneman Treasurer, ACS COMP Division RPI Chemistry Director, RECCR Center From owner-chemistry@ccl.net Fri Oct 17 16:18:00 2008 From: "Chongwen zhou cwzhou2008%a%gmail.com" To: CCL Subject: CCL:G: Error in calculating the single point energy with molpro Message-Id: <-37941-081016175033-20800-pNyWC1sW9ima8J8Rp2H0kQ[A]server.ccl.net> X-Original-From: "Chongwen zhou" Date: Thu, 16 Oct 2008 17:50:29 -0400 Sent to CCL by: "Chongwen zhou" [cwzhou2008[-]gmail.com] I am a newer in using the molpro. The molecule i calculated is an open shell system. I calculated the single point energy by UCCSD(T) method without defining the parameters of wf, open and occ. And the calculation shows that: ?CONVERGENCE NOT REACHED AFTER MAX. ITERATIONS. So the energy at UCCSD(T) level has not been obtained, only the UCCSD energy obtained. Why the result is so? And for a same molecule, the energy obtained by the molpro has higher energy than that obtained by the Gaussian program by the same method. Have you do this calculations? Thank you! lulu Zhou cwzhou2008%%gmail.com From owner-chemistry@ccl.net Fri Oct 17 16:55:02 2008 From: "chongwen zhou cwzhou2008 .. gmail.com" To: CCL Subject: CCL:G: Error in calculating the single point energy with molpro Message-Id: <-37942-081017134107-6697-vWVCzRXQCkhxewZ/S3X8KA]=[server.ccl.net> X-Original-From: "chongwen zhou" Date: Fri, 17 Oct 2008 13:41:03 -0400 Sent to CCL by: "chongwen zhou" [cwzhou2008.-.-.gmail.com] I am a newer in using the molpro. The molecule i calculated is an open shell system. I calculated the single point energy by UCCSD(T) method without defining the parameters of wf, open and occ. And the calculation shows that: ?CONVERGENCE NOT REACHED AFTER MAX. ITERATIONS. So the energy at UCCSD(T) level has not been obtained, only the UCCSD energy obtained. Why the result is so? And for a same molecule, the energy obtained by the molpro has higher energy than that obtained by the Gaussian program by the same method. Have you do this calculations? Thank you! lulu Zhou cwzhou2008-.-gmail.com