There may be another and easier way, = but do you have the optimized structure of the molecule? If so, you c= ould do a single point calculation (at the same level of theory).

Cheers,

Flick Coleman

_______________

William F. Coleman

Professor of Chemistry

Wellesley College

Wellesley MA 02481

www.wellesley.edu/Chemist= ry/colemanw.html

Editor, JCE WebWare and JCE Featured = Molecules

http://www.jce.divched.org/JCE= DLib/WebWare/

h= ttp://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html=

----=_--1dda79eb.1dda79b6.c67fc53c-- From owner-chemistry@ccl.net Sun Jul 12 13:28:01 2009 From: "partha p kundu partha1kundu!A!yahoo.com" To: CCL Subject: CCL:G: raman relative intensity Message-Id: <-39755-090712084943-29756-klFS503TC2zzpfYVLbewHQ ~~ server.ccl.net> X-Original-From: "partha p kundu" Date: Sun, 12 Jul 2009 08:49:40 -0400 Sent to CCL by: "partha p kundu" [partha1kundu]-[yahoo.com] Hi, I am trying to calculate Raman relative intensity from optical activity from Gaussian calculation by multiplying (n-n0)^4/n*C since the exponential term was giving value of 1.But with that the intensity at the lower wavelength was very low compared to the higher wave no. and the data did not match at all with the experimental data.Am I doing any mistake? Please help me. Thanks in advance. Partha. From owner-chemistry@ccl.net Sun Jul 12 14:12:00 2009 From: "Venable, Richard (NIH/NHLBI) E venabler .. nhlbi.nih.gov" To: CCL Subject: CCL: How to calculate the partial charge from quantum mechanism Message-Id: <-39756-090712140945-31686-xS4O7mpTks+17w57CgAFfg[-]server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 12 Jul 2009 14:09:28 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler[*]nhlbi.nih.gov] Not all MM force fields use QM partial charges directly; in some cases the = MM charges may be weighted averages, based on conformational populations, a= nd may be further scaled based on usage assumptions such as an aqueous envi= ronment. Each MM force field tends to have it's own approach, which is hop= efully well documented. -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 7/12/09 3:17 AM, "Marcel Swart marcel.swart#icrea.es" wrote: Sent to CCL by: Marcel Swart [marcel.swart|-|icrea.es] If you want to use them in MD simulations, you want to have charges that give a good description of the electrostatic potential around the molecule. There are several ways to get reasonable values, either by Electro Static Potential (ESP) charges such as Merz-Kollmann, but preferaby more sophisticated methods such as the Multipole Derived Charges in ADF or the RESP charges from Amber. See the Amber website and the related Antechamber pages how to obtain these latter. Quoting "Qing Shao shaoqingfly1981..gmail.com" : > Sent to CCL by: "Qing Shao" [shaoqingfly1981,,gmail.com] > Hi cclers, > I want to calculate the partial charge of some aromatic compound > with quantum mechansim and use them in classical molecular > simulation. As I am newbie in quantum, it would be very appreciate > if anyone could tell me how to get the partial charge from quantum > calculation. I know that we can get Mulliken charge or lowdin > charge. What are the difference between them and the partial charge? > Thanks > Qing > From owner-chemistry@ccl.net Sun Jul 12 16:13:00 2009 From: "Kalju Kahn kalju=-=chem.ucsb.edu" To: CCL Subject: CCL: How to calculate the partial charge from quantum mechanism Message-Id: <-39757-090712160256-28460-lsgLLWhuMBXk7xIY/CuGYg(!)server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 12 Jul 2009 13:02:42 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju/a\chem.ucsb.edu] Qing, In addition to the good replies posted already, please consider the fact that in molecular mechanics charges are usually atom-centered. In aromatic compounds, there is a significant perpendicular component (pi-cloud) that is not well described by points that lie on the aromatic plane. As a result, some properties, such as cation-Pi interactions are difficult to model by off-the-shelf force fields. You can check if your partial charge model reproduces QM potential by calculating the electrostatic potential around the molecule using MM charges, and comparing this to the true QM potential. Visuals at http://www.chem.ucsb.edu/~kalju/chem162/public/smallmol_visual_elpot.html might be helpful. Hope this helps, Kalju > > Sent to CCL by: "Qing Shao" [shaoqingfly1981,,gmail.com] > Hi cclers, > I want to calculate the partial charge of some aromatic compound with > quantum mechansim and use them in classical molecular simulation. As I > am newbie in quantum, it would be very appreciate if anyone could tell > me how to get the partial charge from quantum calculation. I know that > we can get Mulliken charge or lowdin charge. What are the difference > between them and the partial charge? > Thanks > Qing> > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Sun Jul 12 17:38:01 2009 From: "Kalju Kahn kalju:+:chem.ucsb.edu" To: CCL Subject: CCL:G: generating chk point file from output file Message-Id: <-39758-090712163412-8283-AMnHvqgEBU7lD0WFLWn85w{}server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 12 Jul 2009 13:33:58 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju_+_chem.ucsb.edu] Abishek, I do not think it is possible with Gaussian. However, GAMESS and Firefly support Hessians in the input file $HESS block $END. For example, if you have spend lots of time to calculate RHF frequencies, and were hoping to continue to MP2 optimization using this Hessian, you could create an Hessian input block for GAMESS based on your Gaussian output (you need the Hessian, not just frequencies). I think the Hessian is given in the archive section at the very end. Of course, you have to pay attention to the format, and the molecular orientation. Thus, after considerable tinkering with making your $HESS input (has anybody created a script to do this?), you should be able to optimize your structure with GAMESS or Firefly. If you were to do it, it would also make sense to scale the Hessian because the SCF second derivatives are typically too large (that's why HF frequencies are often scaled by 0.90 or so). Sincerely, Kalju > "CCL Subscribers" on Sunday, July 12, 2009 at 6:56 > AM > -0400 wrote: >>I have frequency calculation output of a molecule, but I dont have check >>point of that molecule. >> >>is there is any short procedure(short calculation) to generate chk point >>file of that molecule, without performing again that long frequency >>calculation. >> >> >>Dr. Abhishek Mishra > > > There may be another and easier way, but do you have the optimized > structure of the molecule? If so, you could do a single point calculation > (at the same level of theory). > > Cheers, > > Flick Coleman > > _______________ > William F. Coleman > Professor of Chemistry > Wellesley College > Wellesley MA 02481 > > www.wellesley.edu/Chemistry/colemanw.html > > Editor, JCE WebWare and JCE Featured Molecules > http://www.jce.divched.org/JCEDLib/WebWare/ > http://jchemed.chem.wisc.edu/JCEWWW/Features/MonthlyMolecules/index.html > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106