From owner-chemistry@ccl.net Thu Aug 5 01:54:00 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis[A]borealisgroup.com" To: CCL Subject: CCL:G: Conformation of trication Message-Id: <-42441-100805015251-20798-mbsDk/pSSeJCx7PyT6urxA*server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Aug 2010 07:52:39 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis---borealisgroup.com] Hi Vijay If the minimum energy configuration is the only thing you're interested in any computational chemistry/physics program will do the job. They all work on similar ways and have routines that do the same things (though in different ways but that's beside the point and does not concern you at this stage). If you use quantum mechanical methods (I assume that's what you're looking for) then the only issues you need to think about is which theory level and basis set will be the best and most efficient way for your particular problem. If you are not interested in electronic properties like wavefunctions, orbitals etc you can always use semiempirical methods that are very fast and relatively accurate. Personally I am using Gaussian, but all other software packages available should be able to perform the energy minimisation task without any problems. I hope this helps Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com-,-ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com-,-ccl.net] On Behalf Of Vijay Tak takvijay(~)gmail.com Sent: Wednesday, August 04, 2010 7:42 PM To: Gkourmpis, Thomas Subject: CCL: Conformation of trication Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] Hi CCL, I am very new to computational chemistry. Please help me out.I would like to find the minimum energy conformation of imidazolium based trication ( total 86 atoms).Let me know which software is suitable in this case. Is Discovery studio is appropriate for for this task. Thanks, Vijay Tak takvijay|a|gmail.comhttp://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 Thu Aug 5 03:02:00 2010 From: "Andreas Klamt klamt(!)cosmologic.de" To: CCL Subject: CCL:G: Conformation of trication Message-Id: <-42442-100805025251-32111-+q+IDzBaGlmHrC9Shnf6mg|*|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 05 Aug 2010 08:52:45 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt..cosmologic.de] Hi Vijay, Thomas is basically right, but I think he missed to mention an important aspect, i.e. solvation. It is quite unlikely that you are interested in your trication in vacuum or gasphase. Most likely you are interested in the aqueous solvation. Hence you need to use a combination of a QM with a solvation model. Implicit solvation models are most efficient. I am convinced that COSMO-RS is most reliable in this regard. Years ago some Danish people did a comparison on the accuracy of the prediction of the right conformers of „Conformational analysis of cyclic acidic a-amino acids in aqueous solution - an evaluation of different continuum hydration models." by Peter Aadal Nielsen, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy Liljefors (I am currently not sure whether and where this finally got published.) Several of the species were ions. COSMO-RS had by far the smallest error in this blind prediction test. I am not aware of other method comparisons in this regard. Quite surely there are none for triply charged species. Best regards Andreas Am 05.08.2010 07:52, schrieb Gkourmpis, Thomas Thomas.Gkourmpis[A]borealisgroup.com: > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis---borealisgroup.com] > Hi Vijay > > If the minimum energy configuration is the only thing you're interested in any computational chemistry/physics program will do the job. They all work on similar ways and have routines that do the same things (though in different ways but that's beside the point and does not concern you at this stage). If you use quantum mechanical methods (I assume that's what you're looking for) then the only issues you need to think about is which theory level and basis set will be the best and most efficient way for your particular problem. If you are not interested in electronic properties like wavefunctions, orbitals etc you can always use semiempirical methods that are very fast and relatively accurate. Personally I am using Gaussian, but all other software packages available should be able to perform the energy minimisation task without any problems. > > I hope this helps > > Thomas > > > -----Original Message----- > >> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net] On Behalf Of Vijay Tak takvijay(~)gmail.com >> > Sent: Wednesday, August 04, 2010 7:42 PM > To: Gkourmpis, Thomas > Subject: CCL: Conformation of trication > > > Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] > Hi CCL, > I am very new to computational chemistry. Please help me out.I would like to find the minimum energy conformation of imidazolium based trication ( total 86 atoms).Let me know which software is suitable in this case. Is Discovery studio is appropriate for for this task. > Thanks, > Vijay Tak > takvijay|a|gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > -- PD. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH& Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt**cosmologic.de web www.cosmologic.de HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Thu Aug 5 03:37:01 2010 From: "Kamalakar Jadhav kjadhav[-]vlifesciences.com" To: CCL Subject: CCL: Workshop: Lead Optimization: Changing Technology Perspectives as Cloud Message-Id: <-42443-100805031618-18767-R8K9N5rHGN6PotM3Y4j8wA(_)server.ccl.net> X-Original-From: "Kamalakar Jadhav" Date: Thu, 5 Aug 2010 03:16:10 -0400 Sent to CCL by: "Kamalakar Jadhav" [kjadhav],[vlifesciences.com] Workshop: Lead Optimization: Changing Technology Perspectives as Cloud Computing Where: ACS Fall Exposition, Boston Convention and Exhibition Center, Boston MA Room: 102A When: Wednesday, August 25, 8:30 AM - 11:00 AM Registration Charges: Free Register: http://www.vlifesciences.com/support/ACSWorkshops_2010.php Details: 8.30 AM to 9.15 AM Demonstration would highlight a new perspective on lead optimization as SCOPE (Structure-based compound optimization, prioritization and evolution). 9.30 AM to 10.15 AM We would discuss GQSAR, a practical approach on QSAR pin pointing clues for lead optimization and design. 10.30 AM to 11.00 AM How services like virtual screening can be achieved efficiently via cloud computing? Workshop attendees can also claim for assured gift. ** VLife will be exhibiting SCOPE and GQSAR along with its other technologies at the ACS Fall 2010 National Exposition to be held in Boston, MA between 22nd and 26th August, 2010. We welcome you to booth 1041 to discuss your computational needs in drug discovery and new molecule design.** Thanks, Kamalakar Jadhav VLife Sciences Technologies Pvt. Ltd. From owner-chemistry@ccl.net Thu Aug 5 04:12:01 2010 From: "Dr. apoorva dwivedi apoorvahdi_+_gmail.com" To: CCL Subject: CCL:G: plot a graph between dos and energy in first pronciple calculations Message-Id: <-42444-100805035719-22810-G90lny6ybQ2kk5R0sZPlsw^^server.ccl.net> X-Original-From: "Dr. apoorva dwivedi" Date: Thu, 5 Aug 2010 03:57:16 -0400 Sent to CCL by: "Dr. apoorva dwivedi" [apoorvahdi/./gmail.com] Respected sirs/madams I am a research scholar in computational physics field. i want to know that how to plot a graph between dos and energy in first pronciple calculations and how to calculate magnetic moment from out put of gaussian 03-09 softwares.please guide me in brief. thanks From owner-chemistry@ccl.net Thu Aug 5 04:52:00 2010 From: "YZ Lan lyzhao++zjnu.cn" To: CCL Subject: CCL: Request: second order hyperpolarizability (Gamma) of the C atom Message-Id: <-42445-100805044251-10592-zhVDxiQdsVfV4ii5VEe1zA * server.ccl.net> X-Original-From: "YZ Lan" Date: Thu, 5 Aug 2010 04:42:49 -0400 Sent to CCL by: "YZ Lan" [lyzhao[]zjnu.cn] Dear CCLers, Could you tell me whether there is a report on the static second-order hyperpolarizability (Gamma) of the C atom? Best regards. Youzhao Lan From owner-chemistry@ccl.net Thu Aug 5 07:08:00 2010 From: "Vijay Tak takvijay_-_gmail.com" To: CCL Subject: CCL:G: Conformation of trication Message-Id: <-42446-100805070538-7228-4foyQiu2Kb4opOKG2sgn9g,,server.ccl.net> X-Original-From: "Vijay Tak" Date: Thu, 5 Aug 2010 07:05:37 -0400 Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] Hi Andreas & Thomas, Thank you very much for your reply. Actually I want to calculate the energy of a gas phase adduct between trication and organic anion. For this, first of all, i have to find out low energy aconformation of trication and then try to optimize the structure of adduct between trication and organic anion. I want one clearification from you people. If we find out for example 50 different conformations of trication by using semi-emprical methods and then, minimize thier energy by using a DFT approach, are they shown same or different energy? If they give different energy, then my objective is to find out the enregy of gas phase adduct between the optimized lowest enegy conformation of trication and arganic anion. Please give your suggestions. Best regards Vijay Tak > "Andreas Klamt klamt(!)cosmologic.de" wrote: > > Sent to CCL by: Andreas Klamt [klamt..cosmologic.de] > Hi Vijay, > > Thomas is basically right, but I think he missed to mention an important > aspect, i.e. solvation. It is quite unlikely that you are interested in > your trication in vacuum or gasphase. Most likely you are interested in > the aqueous solvation. Hence you need to use a combination of a QM with > a solvation model. Implicit solvation models are most efficient. I am > convinced that COSMO-RS is most reliable in this regard. > > Years ago some Danish people did a comparison on the accuracy of the > prediction of the right conformers of > Conformational analysis of cyclic acidic a-amino acids in aqueous > solution - an evaluation of different continuum hydration models." > by Peter Aadal Nielsen, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy > Liljefors (I am currently not sure whether and where this finally got > published.) > Several of the species were ions. COSMO-RS had by far the smallest error > in this blind prediction test. I am not aware of other method > comparisons in this regard. Quite surely there are none for triply > charged species. > > Best regards > > Andreas > > > > > Am 05.08.2010 07:52, schrieb Gkourmpis, Thomas > Thomas.Gkourmpis[A]borealisgroup.com: > > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis---borealisgroup.com] > > Hi Vijay > > > > If the minimum energy configuration is the only thing you're interested in any computational chemistry/physics program will do the job. They all work on similar ways and have routines that do the same things (though in different ways but that's beside the point and does not concern you at this stage). If you use quantum mechanical methods (I assume that's what you're looking for) then the only issues you need to think about is which theory level and basis set will be the best and most efficient way for your particular problem. If you are not interested in electronic properties like wavefunctions, orbitals etc you can always use semiempirical methods that are very fast and relatively accurate. Personally I am using Gaussian, but all other software packages available should be able to perform the energy minimisation task without any problems. > > > > I hope this helps > > > > Thomas > > > > > > -----Original Message----- > > > >> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net] On Behalf Of Vijay Tak takvijay(~)gmail.com > >> > > Sent: Wednesday, August 04, 2010 7:42 PM > > To: Gkourmpis, Thomas > > Subject: CCL: Conformation of trication > > > > > > Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] > > Hi CCL, > > I am very new to computational chemistry. Please help me out.I would like to find the minimum energy conformation of imidazolium based trication ( total 86 atoms).Let me know which software is suitable in this case. Is Discovery studio is appropriate for for this task. > > Thanks, > > Vijay Tak > > takvijay|a|gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > > > > > > > -- > PD. Dr. Andreas Klamt > CEO / Geschftsfhrer > COSMOlogic GmbH& Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt**cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamt > > From owner-chemistry@ccl.net Thu Aug 5 08:06:00 2010 From: "YZ Lan lyzhao[*]zjnu.cn" To: CCL Subject: CCL: Request: second order hyperpolarizability (Gamma) of the C at Message-Id: <-42447-100805080408-10674-fgaNHYM2UYdNWeiEK69HVQ##server.ccl.net> X-Original-From: "YZ Lan" Date: Thu, 5 Aug 2010 08:04:07 -0400 Sent to CCL by: "YZ Lan" [lyzhao^zjnu.cn] Dear Prof. P. Atrand, Thank you very much. Best regards. Youzhao Lan Date:2010-08-05 ======================================================== > FromPer-Olof trand Date2010-08-05 18:28:42 Tolyzhao Cc SubjectRe: CCL: Request: second order hyperpolarizability (Gamma) of the C atom Dear Youzhao Lan, I take this off-list. It depends on what you want if for. We have some C parameters in our interaction model. Please, see papers 49, 50, 54, 55, and 71 in my publication list http://www.nt.ntnu.no/users/aastrand/publ.html (where you have links to the papers) and references therein. Per-Olof strand Sitat "YZ Lan lyzhao++zjnu.cn" : > > Sent to CCL by: "YZ Lan" [lyzhao[]zjnu.cn] > Dear CCLers, > Could you tell me whether there is a report on the static > second-order hyperpolarizability (Gamma) of the C atom? > > Best regards. > > Youzhao Lan > > From owner-chemistry@ccl.net Thu Aug 5 08:40:00 2010 From: "bibek salam bibeksalam+*+gmail.com" To: CCL Subject: CCL: convergance problem Message-Id: <-42448-100804112300-21927-biu6mXxyruqyiyLnuwqQDw * server.ccl.net> X-Original-From: "bibek salam" Date: Wed, 4 Aug 2010 11:22:59 -0400 Sent to CCL by: "bibek salam" [bibeksalam,gmail.com] my input file is chk=PMt6_OCT_3.chk %mem=11MW %nproc=1 # opt ub3lyp/lanl2dz geom=connectivity pop=regular Title Card Required 0 3 Pt 2.106939 -0.058575 -0.247726 Pt 0.299835 0.009937 -2.088564 Pt -1.546096 -0.001047 -0.257434 Pt 0.279741 -0.107867 1.562981 Pt 0.237820 -1.864324 -0.327019 Pt 0.303565 1.786939 -0.217402 1 2 1.0 4 1.0 5 1.0 6 1.0 2 3 1.0 5 1.0 6 1.0 3 4 1.0 5 1.0 6 1.0 4 5 1.0 6 1.0 5 6 my output file gives this typpe of message and then convergance failure: Defaulting to unpruned grid for atomic number 78. EnCoef did 4 forward-backward iterations EnCoef did 2 forward-backward iterations EnCoef did 5 forward-backward iterations Rare condition: small coef for last iteration: 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Restarting incremental Fock formation. Matrix for removal 1 Erem= -646.833273673952 Crem= 0.000D+00 Matrix for removal 1 Erem= -655.414391397770 Crem= 0.000D+00 Matrix for removal 2 Erem= -713.706362159628 Crem= 0.000D+00 Matrix for removal 1 Erem= -714.107733589411 Crem= 0.000D+00 Matrix for removal 2 Erem= -714.155879605164 Crem= 0.000D+00 Rare condition: small coef for last iteration: 0.000D+00 Matrix for removal 2 Erem= -714.737559208254 Crem= 0.000D+00 please help me From owner-chemistry@ccl.net Thu Aug 5 09:16:01 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis^borealisgroup.com" To: CCL Subject: CCL:G: Conformation of trication Message-Id: <-42449-100805090600-21328-f7WBaqZVmoUfBgrx3V2Zkw/a\server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Aug 2010 15:05:46 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis=borealisgroup.com] Vijay I am not a chemist so I don't really follow the chemical reaction that you are talking about (at least not without I see it written by someone who does understand it) but the rule of thumb in the energy minimisation is that only the equilibrium structure will have the minimum energy. Now having said that there is a possibility that one particular molecule adopts two or three different conformers. In this case all of them will exist in a local minima, but they will not have the same energy. The differences in energy between the different conformations can give you an indication of the probability of such a conformation to actually exist. With respect to the problem you're asking I assume you need to run the quantum mechanical calculation (DFT) and see what configurations you get for the different conformers. If you do that you can map them with respect to their relative energies and see how different they are. Based on this knowledge you will then make educational guesses on how to proceed and which reaction route is the most probable. Again as I said before I am not a chemist so I might be missing something important here. If this is the case I apologise in advance. What I said works in general for all energy minimisations and the basics are always the same for all types of calculations irrespective of the chemical in question. I hope this helps. If you need more information or if something is not clear please let me know and I will be happy to assist in any way I can Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com++ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com++ccl.net] On Behalf Of Vijay Tak takvijay_-_gmail.com Sent: Thursday, August 05, 2010 1:06 PM To: Gkourmpis, Thomas Subject: CCL:G: Conformation of trication Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] Hi Andreas & Thomas, Thank you very much for your reply. Actually I want to calculate the energy of a gas phase adduct between trication and organic anion. For this, first of all, i have to find out low energy aconformation of trication and then try to optimize the structure of adduct between trication and organic anion. I want one clearification from you people. If we find out for example 50 different conformations of trication by using semi-emprical methods and then, minimize thier energy by using a DFT approach, are they shown same or different energy? If they give different energy, then my objective is to find out the enregy of gas phase adduct between the optimized lowest enegy conformation of trication and arganic anion. Please give your suggestions. Best regards Vijay Tak > "Andreas Klamt klamt(!)cosmologic.de" wrote: > > Sent to CCL by: Andreas Klamt [klamt..cosmologic.de] > Hi Vijay, > > Thomas is basically right, but I think he missed to mention an important > aspect, i.e. solvation. It is quite unlikely that you are interested in > your trication in vacuum or gasphase. Most likely you are interested in > the aqueous solvation. Hence you need to use a combination of a QM with > a solvation model. Implicit solvation models are most efficient. I am > convinced that COSMO-RS is most reliable in this regard. > > Years ago some Danish people did a comparison on the accuracy of the > prediction of the right conformers of > Conformational analysis of cyclic acidic a-amino acids in aqueous > solution - an evaluation of different continuum hydration models." > by Peter Aadal Nielsen, Per-Ola Norrby, Jerzy W. Jaroszewski, and Tommy > Liljefors (I am currently not sure whether and where this finally got > published.) > Several of the species were ions. COSMO-RS had by far the smallest error > in this blind prediction test. I am not aware of other method > comparisons in this regard. Quite surely there are none for triply > charged species. > > Best regards > > Andreas > > > > > Am 05.08.2010 07:52, schrieb Gkourmpis, Thomas > Thomas.Gkourmpis[A]borealisgroup.com: > > Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis---borealisgroup.com] > > Hi Vijay > > > > If the minimum energy configuration is the only thing you're interested in any computational chemistry/physics program will do the job. They all work on similar ways and have routines that do the same things (though in different ways but that's beside the point and does not concern you at this stage). If you use quantum mechanical methods (I assume that's what you're looking for) then the only issues you need to think about is which theory level and basis set will be the best and most efficient way for your particular problem. If you are not interested in electronic properties like wavefunctions, orbitals etc you can always use semiempirical methods that are very fast and relatively accurate. Personally I am using Gaussian, but all other software packages available should be able to perform the energy minimisation task without any problems. > > > > I hope this helps > > > > Thomas > > > > > > -----Original Message----- > > > >> From: owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com() ccl.net] On Behalf Of Vijay Tak takvijay(~)gmail.com > >> > > Sent: Wednesday, August 04, 2010 7:42 PM > > To: Gkourmpis, Thomas > > Subject: CCL: Conformation of trication > > > > > > Sent to CCL by: "Vijay Tak" [takvijay%x%gmail.com] > > Hi CCL, > > I am very new to computational chemistry. Please help me out.I would like to find the minimum energy conformation of imidazolium based trication ( total 86 atoms).Let me know which software is suitable in this case. Is Discovery studio is appropriate for for this task. > > Thanks, > > Vijay Tak > > takvijay|a|gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > > > > > > > > -- > PD. Dr. Andreas Klamt > CEO / Geschftsfhrer > COSMOlogic GmbH& Co. KG > Burscheider Strasse 515 > D-51381 Leverkusen, Germany > > phone +49-2171-731681 > fax +49-2171-731689 > e-mail klamt**cosmologic.de > web www.cosmologic.de > > HRA 20653 Amtsgericht Koeln, GF: Dr. Andreas Klamt > Komplementaer: COSMOlogic Verwaltungs GmbH > HRB 49501 Amtsgericht Koeln, GF: Dr. Andreas Klamthttp://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 Thu Aug 5 09:51:00 2010 From: "Thomas Gkourmpis thomas.gkourmpis(~)borealisgroup.com" To: CCL Subject: CCL:G: Reaction Rate as a function of Pressure Message-Id: <-42450-100805093711-7780-2BfhjfAtIk0rhyuld+gRaQ[-]server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Thu, 5 Aug 2010 09:37:09 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis * borealisgroup.com] Hello everyone I have a question to ask regarding the pressure and temperature dependence on the reaction rate. I am trying to calculate the rate constant of a beta scission in a radical (tertbutoxy radical) obtained by the decomposition of a peroxide. I am using Gaussian for this job and I have no problem in locating the minimum energy configurations for products, reactant(s) and transition states. After the final structures have been obtained I am running a frequency calculation as a function of pressure and temperature to obtain the relevant frequencies, Gibbs Free Energies and partition functions I need for the Arrhenius equation. This is where I have a problem. The frequency outcome as a function of temperature is fine and I have no problems with it, but the pressure outcome is really puzzling. My results seem to indicate that all the thermodynamic quantities that I calculate have almost negligible dependence on pressure (especially the frequencies that remain unchanged for the same temperature). I am interested in temperature ranges of the order 300K-800K and pressures from 1bar to 3000bars. I know from experimental data that the reaction constant does change as a function of pressure (it gets shifted towards the right as pressure increases), but my calculations does not seem to be able to reproduce this phenomenon. One of the reasons I can think about this is the fact that all the thermochemical calculations in Gaussian are done under the Born-Oppenheimer approximation, but I am not sure if this is the only reason (I might be missing something else). Therefore the favour I want to ask is this: Can anyone tell me if this is an effect due only to the approximation I am using? Furthermore if this is the case can anybody please suggest any possible ways to apply corrections to this approximation for high pressures? Thanks a lot in advance Thomas From owner-chemistry@ccl.net Thu Aug 5 10:59:00 2010 From: "Ol Ga eurisco1{=}pochta.ru" To: CCL Subject: CCL: convergance problem Message-Id: <-42451-100805103339-3445-/kftxhU/CjB0ACoR5KYaOQ]*[server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 5 Aug 2010 10:33:36 -0400 Sent to CCL by: "Ol Ga" [eurisco1(!)pochta.ru] Dear Bibek Salam, I would suggest you to add keyword SCF in your input like %mem=11MW <--- possible too low value. You should increase this value as much as possible. %nproc=1 # opt ub3lyp/lanl2dz geom=connectivity pop=regular scf(XQC,vshift=150,Maxcycle=512) Sincerely, Ol Ga PS: actually problem "> Matrix for removal 2 Erem= -714.155879605164 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 2 Erem= -714.737559208254 Crem= 0.000D+00" was discussed here many times. -------------------------------------------------- > From: "bibek salam bibeksalam+*+gmail.com" Sent: Wednesday, August 04, 2010 7:22 PM To: "Ga, Ol " Subject: CCL: convergance problem > > > Sent to CCL by: "bibek salam" [bibeksalam,gmail.com] > my input file is > chk=PMt6_OCT_3.chk > %mem=11MW > %nproc=1 > # opt ub3lyp/lanl2dz geom=connectivity pop=regular > > Title Card Required > > 0 3 > Pt 2.106939 -0.058575 -0.247726 > Pt 0.299835 0.009937 -2.088564 > Pt -1.546096 -0.001047 -0.257434 > Pt 0.279741 -0.107867 1.562981 > Pt 0.237820 -1.864324 -0.327019 > Pt 0.303565 1.786939 -0.217402 > > 1 2 1.0 4 1.0 5 1.0 6 1.0 > 2 3 1.0 5 1.0 6 1.0 > 3 4 1.0 5 1.0 6 1.0 > 4 5 1.0 6 1.0 > 5 > 6 > my output file gives this typpe of message and then convergance failure: > Defaulting to unpruned grid for atomic number 78. > EnCoef did 4 forward-backward iterations > EnCoef did 2 forward-backward iterations > EnCoef did 5 forward-backward iterations > Rare condition: small coef for last iteration: 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Restarting incremental Fock formation. > Matrix for removal 1 Erem= -646.833273673952 Crem= 0.000D+00 > Matrix for removal 1 Erem= -655.414391397770 Crem= 0.000D+00 > Matrix for removal 2 Erem= -713.706362159628 Crem= 0.000D+00 > Matrix for removal 1 Erem= -714.107733589411 Crem= 0.000D+00 > Matrix for removal 2 Erem= -714.155879605164 Crem= 0.000D+00 > Rare condition: small coef for last iteration: 0.000D+00 > Matrix for removal 2 Erem= -714.737559208254 Crem= 0.000D+00 > please help me > > > From owner-chemistry@ccl.net Thu Aug 5 11:34:00 2010 From: "Carlos Alberto Ortega Zu iga caoz96_+_yahoo.es" To: CCL Subject: CCL: Information about Web Servers for Virtual Screening Message-Id: <-42452-100805111851-14404-ok1QO1jr/7O2lUKQkLfXEA++server.ccl.net> X-Original-From: "Carlos Alberto Ortega Zu iga" Date: Thu, 5 Aug 2010 11:18:50 -0400 Sent to CCL by: "Carlos Alberto Ortega Zu iga" [caoz96**yahoo.es] Greetings! Dear CCL users, I am searching web servers for virtual screening because i want evaluate one protein, but only i have found Dock Blaster, There are others server to this purpose? Thanks for your help! From owner-chemistry@ccl.net Thu Aug 5 12:09:00 2010 From: "Tatsiana Kirys nushki++mail.ru" To: CCL Subject: CCL: =?koi8-r?Q?Re=3A_CCL=3A_charmm_energy?= Message-Id: <-42453-100805105533-23871-LnQr5Pgk1qXtSiQI0Y5rVQ**server.ccl.net> X-Original-From: Tatsiana Kirys Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Thu, 05 Aug 2010 18:55:24 +0400 Mime-Version: 1.0 Sent to CCL by: Tatsiana Kirys [nushki%%mail.ru] great! thank you very much for your reply i appreciate it!!! Thu, 5 Aug 2010 01:49:21 +0100 ÐÉÓØÍÏ ÏÔ "Mahmoud A. A. Ibrahim m.ibrahim++compchem.net" : > Dear Tatsiana > I am so sorry, may be my reply wasn't helpful enough, due to I haven't worked with Charmm before and I am not familiar with the default parameters used. > > About radii, yes, the GBSA results change with changing the atomic radii, as I know in AMBER, mbondi2 radii is recommended for GBSA calculation. This point is covered in the paper (Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf) > > Sincerely; > > M. Ibrahm > > > > 2010/8/4 Tatsiana Kirys nushki..mail.ru > > > Sent to CCL by: Tatsiana Kirys [nushki~~mail.ru] > > > > thank you, ill read them! > > Wed, 4 Aug 2010 14:19:59 -0400 ÐÉÓØÍÏ ÏÔ "Venable, Richard (NIH/NHLBI) E venabler|nhlbi.nih.gov" : > > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler[*]nhlbi.nih.gov] > > > Please read the CHARMM documentation files gbsw.doc and gbmv.doc (and references therein) for some ideas about how GB methods work, and why they might have some dependence on radii choices. The GB methods also require different truncation methods and cutoffs than the standard parameter set default methods and cutoffs, which are intended for use with explicit TIP3 water instead of an implicit water model. > > > > Also, please note that it might take a few days for someone associated with the MMTSB suite of perl scripts to answer your posts at www.charmm.org, now that they are finally in the correct forum. And besides, people do tend to take vacations in August ... > > > > Regards, > > > > > -- > > Rick Venable 5635 FL/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 8/4/10 12:08 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: > > > > > > > > Sent to CCL by: Tatsiana Kirys [nushki(0)mail.ru] > > Dear Mr Ibrahim > > > > in case of "gb" the software uses Generalized Born equation and that is why we have additional term "GBEnr" which is as far as i understand electrostatic solvation energy and hence Elec must be vacuum electrostatics. > > > > I'm wondering why would they use different atomic radii(if they did)? in perl script i didnt find any clues for different radius. > > > > > > > > Tue, 3 Aug 2010 21:59:37 +0100 ÐÉÓØÍÏ ÏÔ "Mahmoud A. A. Ibrahim m.ibrahim(~)compchem.net" : > > > > > Dear Tatsiana > > > I don't know what the default method is used when you don't specify gb "-par gb". > > > > > > All what I can do is to inform you that this may be returned to the atomic radii used during the calculation, "different radii give different binding energies > > > > > > In addition to the equation used for solvation free enegy calculation and electrostatic contribution. Sure, Eele will be different, for example, in case of "gb" the software uses Generalized Born equation, and in case of the default option the software uses another equation like Poisson Boltzmann equation, this leads to a variation in the binding energy too. > > > > > > > > > For just a thread to follow: "Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf" > > > > > > > > > Hope it may be helpful > > > > > > Sincerely; > > > > > > M. Ibrahim > > > > > > > > > > > > in addition to the equation used for solvation free energy calculation "Generalized Born in case of GB, or another > > > Tatsiana > > > > > > > 2010/8/3 Tatsiana Kirys nushki~~mail.ru > > > > > > > Sent to CCL by: Tatsiana Kirys [nushki!=!mail.ru] > > > > > > > > I posted it to MMTSB forum at charmm.org (http://www.charmm.org/ubbthreads-7-5-5/ubbthreads.php?ubb=showflat&Number=24980#Post24980) > > > > > > but nobody answers it. > > > > > > I'd appreciate your help! > > > > > > Tatsiana Kirys > > > PhD student in bioinformatics > > > > > > Thu, 29 Jul 2010 18:23:24 -0400 ÐÉÓØÍÏ ÏÔ "Venable, Richard (NIH/NHLBI) E venabler^^^nhlbi.nih.gov" : > > > > > > > > > > > Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler:+:nhlbi.nih.gov] > > > > I suggest posting your question to the MMTSB forum at www.charmm.org > > > > > > > > -- > > > > Rick Venable 5635 FL/T906 > > > > Membrane Biophysics Section > > > > NIH/NHLBI Lab. of Computational Biology > > > > Bethesda, MD 20892-9314 U.S.A. > > > > > > > > > > > > On 7/29/10 4:40 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: > > > > > > > > > > > > > > > > > > > > > Sent to CCL by: "Tatsiana Kirys" [tatsiana%x%ku.edu] > > > > Hi all, > > > > > > > > i calculate protein energy using enrCHARMM.pl script. i run it with gb and without for the same protein file. > > > > > > > > enerCHARMM.pl -out total -log file.log file.pdb > > > > BONDs 92.56954 > > > > ANGLes 336.00337 > > > > UREY-b 24.08096 > > > > DIHEdrals 604.46805 > > > > CMAPs -134.62511 > > > > VDWaals -476.01682 > > > > ELEC -2041.80015 > > > > > > > > > > > > enerCHARMM.pl -out total -par gb -log file_gb.log file.pdb > > > > > > > > BONDs 92.56954 > > > > ANGLes 336.00337 > > > > UREY-b 24.08096 > > > > DIHEdrals 604.46805 > > > > CMAPs -134.62511 > > > > VDWaals -485.01639 > > > > ELEC -2021.31359 > > > > ASP 102.42587 > > > > GBEnr -1479.15727 > > > > > > > > i dont understand why Electrostatic and VdW energy terms are different. Any help will be very appreciated!!!ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/> E-mail to subscribers: CHEMISTRY(!)ccl.net or use:> > > > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net or use> > > > > > > > > > > > > > > > > > > -- > > > Mahmoud A. A. Ibrahim > > > Current Address > > > 7.05, School of Chemistry, > > > The University of Manchester, > > > Oxford Road, Manchester, M13 9PL, > > > United Kingdom. > > > > > > Home Address > > > Chemistry Department, > > > Faculty of Science, > > > Minia University, > > > Minia 61519, > > > Egypt. > > > > > > Contact Information > > > Email: m.ibrahim(!)compchem.net > > > Website: www.compchem.net > > > Fax No.: +20862342601 > > > > > > > > ñ × íÏÅÍ íÉÒÅ - http://my.mail.ru/mail/nushki/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtJade Dynasty - ÒÅ×ÏÌÀÃÉÑ × ÍÉÒÅ ÒÏÌÅ×ÙÈ ÉÇÒ! éÇÒÁÊ ÎÁ Mail.ru! > http://r.mail.ru/cln7681/jd.mail.ru/promo> E-mail to subscribers: CHEMISTRY|,|ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST|,|ccl.net or use> > > > > > > > > -- > Mahmoud A. A. Ibrahim > Current Address > 7.05, School of Chemistry, > The University of Manchester, > Oxford Road, Manchester, M13 9PL, > United Kingdom. > > Home Address > Chemistry Department, > Faculty of Science, > Minia University, > Minia 61519, > Egypt. > > Contact Information > Email: m.ibrahim|,|compchem.net > Website: www.compchem.net > Fax No.: +20862342601 Jade Dynasty - ÏÎÌÁÊÎ-ÉÇÒÁ Ó ÂÅÓËÌÁÓÓÏ×ÏÊ ÓÉÓÔÅÍÏÊ ÒÁÚ×ÉÔÉÑ. ôÅÐÅÒØ × òÏÓÓÉÉ! ôÏÌØËÏ ÎÁ Mail.ru! http://r.mail.ru/cln7683/jd.mail.ru/promo From owner-chemistry@ccl.net Thu Aug 5 12:44:01 2010 From: "John McKelvey jmmckel[a]gmail.com" To: CCL Subject: CCL:G: convergance problem Message-Id: <-42454-100805115629-385-jfV6tO3fFToEnzxvQTowRw-$-server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 5 Aug 2010 11:56:20 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel],[gmail.com] Just wondering... Does Gaussian have "smearing" capabilities in the SCF? This can be very useful when the H-L gap is small and there are many occupied and virtual levels close to the Homo and Lumo. John McKelvey On Thu, Aug 5, 2010 at 10:33 AM, Ol Ga eurisco1{=}pochta.ru wrote: > > Sent to CCL by: "Ol  Ga" [eurisco1(!)pochta.ru] > Dear Bibek Salam, > > I would suggest you to add keyword SCF in your input like > >  %mem=11MW <--- possible too low value. You should increase this value as much as possible. >  %nproc=1 >  # opt ub3lyp/lanl2dz geom=connectivity pop=regular scf(XQC,vshift=150,Maxcycle=512) > > > Sincerely, > Ol Ga > > PS:  actually problem "> Matrix for removal  2 Erem= -714.155879605164     Crem= 0.000D+00 >> Rare condition: small coef for last iteration:  0.000D+00 >> Matrix for removal  2 Erem= -714.737559208254     Crem= 0.000D+00" was discussed here many times. > > > > -------------------------------------------------- >> From: "bibek salam bibeksalam+*+gmail.com" > Sent: Wednesday, August 04, 2010 7:22 PM > To: "Ga, Ol " > Subject: CCL: convergance problem > >> >> >> Sent to CCL by: "bibek  salam" [bibeksalam,gmail.com] >> my input file is >> chk=PMt6_OCT_3.chk >> %mem=11MW >> %nproc=1 >> # opt ub3lyp/lanl2dz geom=connectivity pop=regular >> >> Title Card Required >> >> 0  3 >> Pt                 2.106939   -0.058575   -0.247726 >> Pt                 0.299835    0.009937   -2.088564 >> Pt                -1.546096   -0.001047   -0.257434 >> Pt                 0.279741   -0.107867    1.562981 >> Pt                 0.237820   -1.864324   -0.327019 >> Pt                 0.303565    1.786939   -0.217402 >> >> 1  2 1.0  4 1.0  5 1.0  6 1.0 >> 2  3 1.0  5 1.0  6 1.0 >> 3  4 1.0  5 1.0  6 1.0 >> 4  5 1.0  6 1.0 >> 5 >> 6 >> my output file gives this typpe of message and then convergance failure: >> Defaulting to unpruned grid for atomic number  78. >> EnCoef did     4 forward-backward iterations >> EnCoef did     2 forward-backward iterations >> EnCoef did     5 forward-backward iterations >> Rare condition: small coef for last iteration:  0.000D+00 >> Rare condition: small coef for last iteration:  0.000D+00 >> Restarting incremental Fock formation. >> Matrix for removal  1 Erem= -646.833273673952     Crem= 0.000D+00 >> Matrix for removal  1 Erem= -655.414391397770     Crem= 0.000D+00 >> Matrix for removal  2 Erem= -713.706362159628     Crem= 0.000D+00 >> Matrix for removal  1 Erem= -714.107733589411     Crem= 0.000D+00 >> Matrix for removal  2 Erem= -714.155879605164     Crem= 0.000D+00 >> Rare condition: small coef for last iteration:  0.000D+00 >> Matrix for removal  2 Erem= -714.737559208254     Crem= 0.000D+00 >> please help me>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel__gmail.com From owner-chemistry@ccl.net Thu Aug 5 13:19:01 2010 From: "Geoffrey Hutchison geoffh-*-pitt.edu" To: CCL Subject: CCL:G: convergance problem Message-Id: <-42455-100805130817-16892-Sn+hYpE3sXTOKeEMHncZvg===server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=us-ascii Date: Thu, 05 Aug 2010 13:08:03 -0400 MIME-version: 1.0 (Apple Message framework v1081) Sent to CCL by: Geoffrey Hutchison [geoffh,pitt.edu] > Just wondering... Does Gaussian have "smearing" capabilities in the > SCF? This can be very useful when the H-L gap is small and there are > many occupied and virtual levels close to the Homo and Lumo. There are a variety of SCF convergence methods. What John suggested here is "Fermi" broadening. In Gaussian, this also includes damping and level shifting -- all three are useful to help with SCF convergence. http://gaussian.com/g_tech/g_ur/k_scf.htm So that might include: SCF(Fermi, XQC,vshift=150,Maxcycle=512) Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh()pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Thu Aug 5 14:16:01 2010 From: "Ol Ga eurisco1 * pochta.ru" To: CCL Subject: CCL:G: convergance problem Message-Id: <-42456-100805135856-6594-aatjBOzIlQH45tlR47atXw .. server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 5 Aug 2010 13:58:54 -0400 Sent to CCL by: "Ol Ga" [eurisco1(_)pochta.ru] Dear John McKelvey, Just a short answer. ) Fermi broadening is a keyword of SCF group. For k-point integration several schemes are applicable by means IOp(5/74). Sincerely, Ol Ga -------------------------------------------------- > From: "John McKelvey jmmckel[a]gmail.com" Sent: Thursday, August 05, 2010 7:56 PM To: "Ga, Ol " Subject: CCL:G: convergance problem > > > Sent to CCL by: John McKelvey [jmmckel],[gmail.com] > Just wondering... Does Gaussian have "smearing" capabilities in the > SCF? This can be very useful when the H-L gap is small and there are > many occupied and virtual levels close to the Homo and Lumo. > > John McKelvey > > On Thu, Aug 5, 2010 at 10:33 AM, Ol Ga eurisco1{=}pochta.ru > wrote: >> >> Sent to CCL by: "Ol Ga" [eurisco1(!)pochta.ru] >> Dear Bibek Salam, >> >> I would suggest you to add keyword SCF in your input like >> >> %mem=11MW <--- possible too low value. You should increase this value as much as possible. >> %nproc=1 >> # opt ub3lyp/lanl2dz geom=connectivity pop=regular scf(XQC,vshift=150,Maxcycle=512) >> >> >> Sincerely, >> Ol Ga >> >> PS: actually problem "> Matrix for removal 2 Erem= -714.155879605164 Crem= 0.000D+00 >>> Rare condition: small coef for last iteration: 0.000D+00 >>> Matrix for removal 2 Erem= -714.737559208254 Crem= 0.000D+00" was discussed here many times. >> >> >> >> -------------------------------------------------- >>> From: "bibek salam bibeksalam+*+gmail.com" >> Sent: Wednesday, August 04, 2010 7:22 PM >> To: "Ga, Ol " >> Subject: CCL: convergance problem >> >>> >>> >>> Sent to CCL by: "bibek salam" [bibeksalam,gmail.com] >>> my input file is >>> chk=PMt6_OCT_3.chk >>> %mem=11MW >>> %nproc=1 >>> # opt ub3lyp/lanl2dz geom=connectivity pop=regular >>> >>> Title Card Required >>> >>> 0 3 >>> Pt 2.106939 -0.058575 -0.247726 >>> Pt 0.299835 0.009937 -2.088564 >>> Pt -1.546096 -0.001047 -0.257434 >>> Pt 0.279741 -0.107867 1.562981 >>> Pt 0.237820 -1.864324 -0.327019 >>> Pt 0.303565 1.786939 -0.217402 >>> >>> 1 2 1.0 4 1.0 5 1.0 6 1.0 >>> 2 3 1.0 5 1.0 6 1.0 >>> 3 4 1.0 5 1.0 6 1.0 >>> 4 5 1.0 6 1.0 >>> 5 >>> 6 >>> my output file gives this typpe of message and then convergance failure: >>> Defaulting to unpruned grid for atomic number 78. >>> EnCoef did 4 forward-backward iterations >>> EnCoef did 2 forward-backward iterations >>> EnCoef did 5 forward-backward iterations >>> Rare condition: small coef for last iteration: 0.000D+00 >>> Rare condition: small coef for last iteration: 0.000D+00 >>> Restarting incremental Fock formation. >>> Matrix for removal 1 Erem= -646.833273673952 Crem= 0.000D+00 >>> Matrix for removal 1 Erem= -655.414391397770 Crem= 0.000D+00 >>> Matrix for removal 2 Erem= -713.706362159628 Crem= 0.000D+00 >>> Matrix for removal 1 Erem= -714.107733589411 Crem= 0.000D+00 >>> Matrix for removal 2 Erem= -714.155879605164 Crem= 0.000D+00 >>> Rare condition: small coef for last iteration: 0.000D+00 >>> Matrix for removal 2 Erem= -714.737559208254 Crem= 0.000D+00 >>> please help me> >> >> > > > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel=gmail.com >