From owner-chemistry@ccl.net Thu Aug 16 02:44:00 2007 From: "Andreas Klamt klamt:cosmologic.de" To: CCL Subject: CCL: solvent calc. Message-Id: <-34939-070816024150-14119-htjth6KDOE13Obn5B+J3vg:-:server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 16 Aug 2007 08:41:11 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt[*]cosmologic.de] Hi Keith, normally the difference between solution phase and gasphase geometries is small. For consistency of the frequency calculations (which should be done in a local minimum geometry) you should do it on the gasphase geometry. More important than the change in geometry is the change in the kind of conformation which is the minimum in gasphase and solution (may be specific for each solvent). Within our COSMO-RS (COSMOtherm) methods I suggest the following procedure: 1) find the relevant conformations of the compounds (educts and products) in the gasphase and in the solvent and calculate their total energy with geometry optimization in the gasphase and in a virtual conductor (DFT/COSMO). We use BP-TZVP for this step. 2) Then get the total free energies of the compound in the gasphase and in the solvent (may even be a mixture, at variable temperature) from COSMOtherm (which also includes the Boltzmann averaging over the conformations). A potential shift in the preferred conformations in gasphase and solution is automatically taken into account in this step. 3) Now perform frequency calculations (probably good enough at DFT level) and higher lever calculations (if affordable, since DFT is unreliable for free energies of reactions) for the relevant conformations (Maybe the lowest conformers are sufficient in this step). 4) Finally correct the free energy of reaction (difference of educts and products) yielded from COSMOtherm by the difference of the vibrational contributions, and by the higher level to DFT differences of the representatives of educts and products taken into account in the higher level calculations. Andreas Keith Butler keeeto2000..yahoo.co.uk schrieb: > Sent to CCL by: Keith Butler [keeeto2000- -yahoo.co.uk] > > Dear Andreas, > > Just a follow up question to your answer. Would you > suggest that to find free energy of the solvated > species using an implict method that the frequency > calculations should be performed in the gas phase on > the SOLUTION phase geometries or on gas phase > structures before applying the thermodynamic cycle. > > Many Thanks, > > Keith Butler > > --- "Andreas Klamt klamt:-:cosmologic.de" > wrote: > > >> Sent to CCL by: Andreas Klamt >> [klamt###cosmologic.de] >> Dear Aleksandra, >> >> sorry to tell you that even in the case of neutral >> reactions it does not >> make much sense to apply the standard gasphase >> methods. All the >> vibrational free energy contributions are not >> meaningful in the solvent. >> The change in vibrational free energy from gasphase >> to the solvent is >> already parameterized into the solvent models (see >> e.g. my CCL >> contribution from 17.05.2007 ). >> >> In my opinion, the only reasonable way to do this in >> the solvent is to >> calculate the gasphase reaction and to apply >> dG_solvation (from a good, >> quantitative solvation model) to educts and >> products., i.e. use the >> thermodynamic cycle >> >> Educts, solv ---> Educts, gas --> Products,gas --> >> Products, solv >> >> Andreas >> >> >> Aleksandra Rudnitskaya aleksandra.rudnit001#umb.edu >> schrieb: >> >>> Sent to CCL by: "Aleksandra Rudnitskaya" >>> >> [aleksandra.rudnit001##umb.edu] >> >>> Thanks a lot to everyone who sent his answer. I >>> >> realized I took a wrong example. What if I choose >> the other system with benzene as a solvent? The >> questions are the same - >> >>> what should I write in input file for >>> >> optimization, and TS? >> >>> Thank you >>> >>> Aleksandra >>> >>> >>> >>>> Dear CCL members, >>>> >>>> Ive just started calculations with solvent. I >>>> >> decided to start from reaction of neutralization >> NaOH+HCl=H2O+NaCl. As I understand I should >> calculate >> >>>> 1) optimization sodium hydroxide in solvent >>>> >> (water); >> >>>> 2) optimization hydrochloric acid in solvent; >>>> 3) optimization sodium chloride in solvent; >>>> 4) transition state again in solvent. >>>> Idea is very similar to that when I calculate >>>> >> rxns in gas phase. Is it correct? >> >>>> When I calculate stable species without any >>>> >> solvent I use >> >>>> opt freq=noraman RHF/6-31G(d) >>>> For TS calculations I use >>>> RHF/6-31G(d) Opt(TS,CalcFC,noeigentest) >>>> >> Freq=noraman >> >>>> and then charge and multiplicity, and simple >>>> >> Z-matrix in specification part. How should input >> files look for optimization and searching TS? I know >> I have to use keyword SCRF, and one of those >> (SCRF=Dipole, PCM, DPCM, CPCM or IEFPCM), then >> specify solvent, and probably, dielectric constant >> somewhere in specification part after matrix. If you >> may guide me how to create input file itll help a >> lot. >> >>>> Thank you very much.> >>>> >>> >>> >>> >> -- >> >> > ----------------------------------------------------------------------------- > >> Dr. habil. Andreas Klamt >> COSMOlogic GmbH&CoKG >> Burscheider Str. 515 >> 51381 Leverkusen, Germany >> >> Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 >> e-mail: klamt[A]cosmologic.de >> web: www.cosmologic.de >> >> > ----------------------------------------------------------------------------- > >> COSMOlogic >> Your Competent Partner for >> Computational Chemistry and Fluid >> Thermodynamics >> >> > ----------------------------------------------------------------------------- > >> >> -= 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.> >> E-mail to administrators: CHEMISTRY-REQUEST : ccl.net >> or use> >> Before posting, check wait time at: >> http://www.ccl.net> Conferences: >> >> > http://server.ccl.net/chemistry/announcements/conferences/ > >> Search Messages: http://www.ccl.net/htdig (login: >> ccl, Password: search) >> >> If your mail bounces from CCL with 5.7.1 error, >> check:> >> RTFI: >> http://www.ccl.net/chemistry/aboutccl/instructions/> >> >> >> >> > > > > ___________________________________________________________ > Yahoo! Answers - Got a question? Someone out there knows the answer. Try it > now. > http://uk.answers.yahoo.com/> > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt=-=cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Thu Aug 16 07:49:01 2007 From: "immanuel feng feng.immanuel/a\gmail.com" To: CCL Subject: CCL:G: convergence failure with pop=nobread Message-Id: <-34940-070815033646-14445-SKFtHg0cfiMWpM46Yk+oGw%%server.ccl.net> X-Original-From: "immanuel feng" Content-Type: multipart/alternative; boundary="----=_Part_30328_27886.1187159756574" Date: Wed, 15 Aug 2007 14:35:56 +0800 MIME-Version: 1.0 Sent to CCL by: "immanuel feng" [feng.immanuel:+:gmail.com] ------=_Part_30328_27886.1187159756574 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, I tried to perform the NBO analysis on the radical cation with ROB3LYP/6-311G(d,p) pop=nboread. The structure is some aromatic six-membered heterocyclic hydroxyl. the output is here: SCF Done: E(ROB+HF-LYP) = -371.234346792 A.U. after 129 cycles Convg = 0.9267D-02 -V/T = 2.0100 S**2 = 0.7500 KE= 3.675742463760D+02 PE=-1.429641058322D+03 EE= 4.027813852709D+02 Annihilation of the first spin contaminant: S**2 before annihilation 0.7500, after 0.7500 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/g03/l502.exe at Tue Jun 13 21:57:44 2006. Job cpu time: 0 days 0 hours 20 minutes 28.3 seconds. File lengths (MBytes): RWF= 20 Int= 0 D2E= 0 Chk= 1 Scr= 1 I've also tried to basis set to 6-31G(d), but convergence was still failure. Could anyone give some advice? Thank you! ------=_Part_30328_27886.1187159756574 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi, I tried to perform the NBO analysis on the radical cation with ROB3LYP/6-311G(d,p) pop=nboread. The structure is some aromatic six-membered heterocyclic hydroxyl. the output is here:
 
SCF Done:  E(ROB+HF-LYP) =  -371.234346792     A.U. after  129 cycles
             Convg  =    0.9267D-02             -V/T =  2.0100
             S**2   =   0.7500
 KE= 3.675742463760D+02 PE=-1.429641058322D+03 EE= 4.027813852709D+02
 Annihilation of the first spin contaminant:
 S**2 before annihilation     0.7500,   after     0.7500
 Convergence failure -- run terminated.
 Error termination via Lnk1e in /usr/g03/l502.exe at Tue Jun 13 21:57:44 2006.
 Job cpu time:  0 days  0 hours 20 minutes 28.3 seconds.
 File lengths (MBytes):  RWF=     20 Int=      0 D2E=      0 Chk=      1 Scr=      1
 
I've also tried to basis set to 6-31G(d), but convergence was still failure. Could anyone give some advice? Thank you!
------=_Part_30328_27886.1187159756574-- From owner-chemistry@ccl.net Thu Aug 16 13:45:01 2007 From: "Barry Hardy barry.hardy===vtxmail.ch" To: CCL Subject: CCL: Best Practices in Virtual Screening Message-Id: <-34941-070816133644-11698-DpuOjxH2pCKBFTqt0Z8frQ\a/server.ccl.net> X-Original-From: Barry Hardy Content-Type: multipart/alternative; boundary="------------060009050105080802070503" Date: Thu, 16 Aug 2007 19:35:52 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy[]vtxmail.ch] This is a multi-part message in MIME format. --------------060009050105080802070503 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Perhaps the most frequent topic of discussion that I have seen consistently arising in my recent conversations with drug discovery researchers, is the topic of Virtual Screening and its complexities, confusions, and varying validity and reliability. John Irwin and I initiated the idea of a best practice initiative last Autumn (http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html). We realise this will take time but I belief it is an endeavour worth undertaking that will be of significant benefit to both industry and academic researchers. To this end we are supporting workshop and wiki activity this Autumn to initiate such a program. The Virtual Screening Community of Practice Workshop and Forum will take place 15-16 October at Bryn Mawr, Philadelphia to further the above goals. This activity will consist of the following components: 1. Workshop to share experiences on current practices in virtual screening and to collaboratively develop best practices for comparison studies. (morning/afternoon of October 15). 2. Conference session on latest method developments with presentations and panel discussion. (October 16) 3. Poster Session (evening of October 16). NOTE: If interested in presenting a poster, please send an abstract (ca. 300-500 words) for review to eCheminfo (-at-) douglasconnect.com We have also left space on the program schedule to feature a selection of the abstracts submitted as oral presentations. 4. Virtual communication and collaboration approaches will be used pre- and post-event to maximise the benefit of the workshop activity. In particular a wiki will be opened prior to the workshop to commence documentation of supporting materials and to start to populate the area with initial suggestions, ideas, practices and methods. The wiki will also support subsequent practice group activities and development initiatives, including future ongoing meetings and workshops and research and development projects. (Realising this activity needs to be in progress for quite some time.) The agenda of workshop will be designed so as to maximise interaction, discussion, issue resolution, and action plans for cooperation. Workshop activities will address the specific challenges: * statistically significant relationships between docking scores and ligand affinity * practices and procedures for the operation of community-based screening and docking comparisons including tests and interpretation of results, in a way that everyone can agree is fair. * peer review, data compilation, running of programs, judgement of results * workflow descriptions for comparisons * beyond conformational energetics in the rank ordering of diverse compounds in high throughput virtual screening * measurement and benchmarking * binding mode prediction, virtual screening for lead identification, rank-ordering by affinity for lead optimization * atom typing, ligand preparation (ionic forms, tautomers, ...), ligand conformer generation, protein preparation (protonation, residue orientation, ...), ligand placement (top-down, bottom-up, fragment based, group based, ...), energy calculation (force field type, grid type, algorithm, ...), constraint handling (global and local optimization strategy? process to escape local minima?), scoring (single-objective, multi-objective, consensus, ...) * separation of test set information from model development * validation datasets, results and applicability domains * objective comparisons of standardized test datasets * extraction of data from the scientific literature * methods and procedures for secure testing of commercial data that could be acceptable to industry * frameworks for computational model testing and validation * impact of knowledge management approaches * collaboration and community support structures and environments We welcome the collaboration and participation of all academic, government and industry practitioners in drug discovery in strengthening the scientific foundations of this valuable set of cheminformatics techniques. More Information Website: http://www.echeminfo.com/COMTY_screeningforumbm07 Pdf Download: http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr07-web1.PDF best regards Barry Hardy eCheminfo Community of Practice Barry Hardy, PhD Douglas Connect Zeiningen, CH-4314 Switzerland Tel: +41 61 851 0170 Blog: http://barryhardy.blogs.com/cheminfostream/ --------------060009050105080802070503 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit

Perhaps the most frequent topic of discussion that I have seen consistently arising in my recent conversations with drug discovery researchers, is the topic of Virtual Screening and its complexities, confusions, and varying validity and reliability.  John Irwin and I initiated the idea of a best practice initiative last Autumn (http://barryhardy.blogs.com/cheminfostream/2006/10/could_we_take_a.html).  We realise this will take time but I belief it is an endeavour worth undertaking that will be of significant benefit to both industry and academic researchers.  To this end we are supporting workshop and wiki activity this Autumn to initiate such a program.

The Virtual Screening Community of Practice Workshop and Forum will take place 15-16 October at Bryn Mawr, Philadelphia to further the above goals.  This activity will consist of the following components:

1. Workshop to share experiences on current practices in virtual screening and to collaboratively develop best practices for comparison studies. (morning/afternoon of October 15).
2. Conference session on latest method developments with presentations and panel discussion. (October 16)
3. Poster Session (evening of October 16). NOTE: If interested in presenting a poster, please send an abstract (ca. 300-500 words) for review to eCheminfo (-at-) douglasconnect.com We have also left space on the program schedule to feature a selection of the abstracts submitted as oral presentations.
4. Virtual communication and collaboration approaches will be used pre- and post-event to maximise the benefit of the workshop activity. In particular a wiki will be opened prior to the workshop to commence documentation of supporting materials and to start to populate the area with initial suggestions, ideas, practices and methods. The wiki will also support subsequent practice group activities and development initiatives, including future ongoing meetings and workshops and research and development projects. (Realising this activity needs to be in progress for quite some time.)

The agenda of workshop will be designed so as to maximise interaction, discussion, issue resolution, and action plans for cooperation. Workshop activities will address the specific challenges:
* statistically significant relationships between docking scores and ligand affinity
* practices and procedures for the operation of community-based screening and docking comparisons including tests and interpretation of results, in a way that everyone can agree is fair.
* peer review, data compilation, running of programs, judgement of results
* workflow descriptions for comparisons
* beyond conformational energetics in the rank ordering of diverse compounds in high throughput virtual screening
* measurement and benchmarking
* binding mode prediction, virtual screening for lead identification, rank-ordering by affinity for lead optimization
* atom typing, ligand preparation (ionic forms, tautomers, ...), ligand conformer generation, protein preparation (protonation, residue orientation, ...), ligand placement (top-down, bottom-up, fragment based, group based, ...), energy calculation (force field type, grid type, algorithm, ...), constraint handling (global and local optimization strategy? process to escape local minima?), scoring (single-objective, multi-objective, consensus, ...)
* separation of test set information from model development
* validation datasets, results and applicability domains
* objective comparisons of standardized test datasets
* extraction of data from the scientific literature
* methods and procedures for secure testing of commercial data that could be acceptable to industry
* frameworks for computational model testing and validation
* impact of knowledge management approaches
* collaboration and community support structures and environments

We welcome the collaboration and participation of all academic, government and industry practitioners in drug discovery in strengthening the scientific foundations of this valuable set of cheminformatics techniques.

More Information
Website: http://www.echeminfo.com/COMTY_screeningforumbm07
Pdf Download: http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr07-web1.PDF


best regards
Barry Hardy
eCheminfo Community of Practice

Barry Hardy, PhD
Douglas Connect
Zeiningen, CH-4314
Switzerland
Tel: +41 61 851 0170
Blog: http://barryhardy.blogs.com/cheminfostream/


--------------060009050105080802070503-- From owner-chemistry@ccl.net Thu Aug 16 14:40:00 2007 From: "Cory Pye cpye===crux.smu.ca" To: CCL Subject: CCL:G: convergence failure with pop=nobread Message-Id: <-34942-070816103328-2585-m6VWmdFjB/aCbWohtgqdOA__server.ccl.net> X-Original-From: Cory Pye Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 16 Aug 2007 10:53:32 -0300 (ADT) MIME-Version: 1.0 Sent to CCL by: Cory Pye [cpye::crux.smu.ca] Hi, I would suggest trying a ROHF/STO-3G, UHF/STO-3G, or maybe a UBLYP or ROBLYP equivalent first, to get a converged wavefunction. Then use guess=read in the 6-31G(d) calculation to read in the converged wavefunction from the checkpoint file. If The STO-3G calcs don't converge, then you can use the more robust but expensive methods (e.g. SCF=QC) at the lower level, and then read that guess in. -Cory On Wed, 15 Aug 2007, immanuel feng feng.immanuel/agmail.com wrote: > Hi, I tried to perform the NBO analysis on the radical cation with > ROB3LYP/6-311G(d,p) pop=nboread. The structure is some aromatic six-membered > heterocyclic hydroxyl. the output is here: > > SCF Done: E(ROB+HF-LYP) = -371.234346792 A.U. after 129 cycles > Convg = 0.9267D-02 -V/T = 2.0100 > S**2 = 0.7500 > KE= 3.675742463760D+02 PE=-1.429641058322D+03 EE= 4.027813852709D+02 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.7500, after 0.7500 > Convergence failure -- run terminated. > Error termination via Lnk1e in /usr/g03/l502.exe at Tue Jun 13 21:57:44 > 2006. > Job cpu time: 0 days 0 hours 20 minutes 28.3 seconds. > File lengths (MBytes): RWF= 20 Int= 0 D2E= 0 Chk= 1 > Scr= 1 > > I've also tried to basis set to 6-31G(d), but convergence was still failure. > Could anyone give some advice? Thank you! > ************* ! Dr. Cory C. Pye ***************** ! Associate Professor *** ** ** ** ! Theoretical and Computational Chemistry ** * **** ! Department of Chemistry, Saint Mary's University ** * * ! 923 Robie Street, Halifax, NS B3H 3C3 ** * * ! cpye\a/crux.stmarys.ca http://apwww.stmarys.ca/~cpye *** * * ** ! Ph: (902)-420-5654 FAX:(902)-496-8104 ***************** ! ************* ! Les Hartree-Focks (Apologies to Montreal Canadien Fans) From owner-chemistry@ccl.net Thu Aug 16 15:13:01 2007 From: "JunJun Liu ljjlp03_-_gmail.com" To: CCL Subject: CCL:G: question about link atom's scale factor of ONIOM in G03 Message-Id: <-34943-070816144526-10085-pt7kvjzBHPM8Vocc6i1qPw()server.ccl.net> X-Original-From: "JunJun Liu" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; delsp=yes; charset=utf-8 Date: Thu, 16 Aug 2007 13:44:59 -0400 MIME-Version: 1.0 Sent to CCL by: "JunJun Liu" [ljjlp03 ~ gmail.com] Hi all, In ONIOM method, when model system(QM part) is built, a set of link atoms(hydrogen atoms) are added to make the model system a close shell. The link atoms are placed based on the following equation: r(link)=r(qm) + g*[r(MM)-r(qm)] where, g is called scale factor or distance parameter. My question is, since G03 determines r(link) automatically, where/how can I know the value of "g" scale factor from the G03 output file? Thanks! JunJun Liu From owner-chemistry@ccl.net Thu Aug 16 17:07:01 2007 From: "Sten Nilsson Lill stenil,,chem.gu.se" To: CCL Subject: CCL:G: question about link atom's scale factor of ONIOM in G03 Message-Id: <-34944-070816165953-16537-L5MbiNvLYfx2kp/G8NBI0Q%%server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 16 Aug 2007 21:58:43 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil{:}chem.gu.se] Hi JunJun, you can find information on the scale factor in the G03 output. Typically it looks like: ----------- (Enter /usr/local/gss/g03/g03/l120.exe) ONIOM: Cut between C /H 21 and C 25 factor= 0.723886 0.723886 etc etc Leave Link 120 --------------- where in this case 0.723886 is the scale factor. You might need to use #p in your route card to get that information printed in the output file. Hope it helps! Regards, Sten Nilsson Lill > > Sent to CCL by: "JunJun Liu" [ljjlp03 ~ gmail.com] > Hi all, > > In ONIOM method, when model system(QM part) is built, a set of link > atoms(hydrogen atoms) are added to make the model system a close shell. > The link atoms are placed based on the following equation: > > r(link)=r(qm) + g*[r(MM)-r(qm)] > > where, g is called scale factor or distance parameter. > > My question is, since G03 determines r(link) automatically, where/how can > I know the value of "g" scale factor from the G03 output file? > > Thanks! > > JunJun Liu> > > > Ph. D. Sten Nilsson Lill Dep. of Chemistry Göteborg University Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2901 Fax: +46-31-772 3840 E-mail: stenil!^!chem.gu.se Alternative e-mail: slill1!^!lsu.edu From owner-chemistry@ccl.net Thu Aug 16 22:34:01 2007 From: "Steven ccl * mail.sioc.ac.cn" To: CCL Subject: CCL: Is there any free solubility prediction software Message-Id: <-34945-070816111221-18123-WDkPbahUhko+qyysdXN49g(!)server.ccl.net> X-Original-From: "Steven" Content-Type: multipart/alternative; boundary="=====003_Dragon188210842745_=====" Date: Thu, 16 Aug 2007 22:39:46 +0800 Mime-Version: 1.0 Sent to CCL by: "Steven" [ccl%mail.sioc.ac.cn] This is a multi-part message in MIME format. --=====003_Dragon188210842745_===== Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit Hi everyone, Is there any free software to calculate the solubility of small organic molecules? Any online web server on this point is also appreciated. Thank you Steven 2007-08-16 --=====003_Dragon188210842745_===== Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: 7bit
Hi everyone,
 
Is there any free software to calculate the solubility of small organic molecules?
Any online web server on this point is also appreciated.
 
Thank you
 
Steven
2007-08-16
 --=====003_Dragon188210842745_=====--