From owner-chemistry@ccl.net Fri Apr 6 00:28:01 2007 From: "Josef Scheiber mail|a|josef-scheiber.de" To: CCL Subject: CCL: Animation of alpha helix wanted Message-Id: <-33983-070405223944-7513-dz+GzsOfQ9LzAlroFWm7PQ(~)server.ccl.net> X-Original-From: Josef Scheiber Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 05 Apr 2007 22:07:31 -0400 MIME-Version: 1.0 Sent to CCL by: Josef Scheiber [mail|josef-scheiber.de] Hi Don, maybe this can help you: http://www-cgi.uni-regensburg.de/Klinik/FunktionelleGenomik/Compdiag/structure/fold.html Best, Sepp Donald J. Keidel keided01:ucr.edu wrote: > Sent to CCL by: "Donald J. Keidel" [keided01**ucr.edu] > > I am looking for an animation that someone might have or know whwere to > download that shows a protein going from primary structure to alpha helix. > I wanted to use it in my course to illustrate how the hydrogen bonding > pattern develops. I have searched the net with no luck. Thank you in > advance for all suggestions. > > Don Keidel> > > From owner-chemistry@ccl.net Fri Apr 6 03:15:02 2007 From: "Michel Petitjean ptitjean##itodys.jussieu.fr" To: CCL Subject: CCL: qsar volume calculation using hyperchem/other software Message-Id: <-33984-070406031108-29566-Iy2XdyyYuzVn9VL/n29VOg#,#server.ccl.net> X-Original-From: Michel Petitjean Date: Fri, 6 Apr 2007 09:10:57 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean[A]itodys.jussieu.fr] To: chemistry*ccl.net Subj: CCL: Re: qsar volume calculation using hyperchem/other software ASV computes van der Waals volumes and more generally volumes of any union of spheres, including the cases of augmented atomic spheres. You can download ASV for free: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Radii are read as an input data. ASV may be called interactively or via script on linux, macosx,.... However, no Windows version is available. Michel Petitjean, Email: petitjean*itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean*ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html Sent to CCL by: "Shivani Syal" [ssyal[-]purdue.edu] > Hi everyone, > > I'm trying to write an excel macro/hcl script to automate > solvent-excluded volume calculations using hyperchem > but I'm having errors running it. Hperchem is not executing > simple commands like 'qsar-property volume' using either DDE > (via excel) or hcl scripts. In short, it is opening the dialog box > but not changing the default option and performing the calculation. > Does anyone have experience with a similar issue or know if > such a functionality (doing batch calculations using the qsar module) > is even possible in hyperchem? If not, can someone recommend a reliable > software/program which gives the flexibility of computing volumes > for different probe radii.(I'm not posting my script here for brevity reasons, > but would be glad to do do if someone has any experience with the same). > > Thanks, > Shivani From owner-chemistry@ccl.net Fri Apr 6 06:25:01 2007 From: "John Simmie john.simmie#,#nuigalway.ie" To: CCL Subject: CCL: Finding a TS Message-Id: <-33985-070406055821-30811-NXVUFQMkJxJrZAOhMO38ng!A!server.ccl.net> X-Original-From: "John Simmie" Date: Fri, 6 Apr 2007 05:58:17 -0400 Sent to CCL by: "John Simmie" [john.simmie:-:nuigalway.ie] TSs can be tricky to find but a quick search of the literature via Web of Science reveals a published geometry for methane + hydroxyl [J Chem Soc Farad Trans 1996 92, page 3468] at differing levels of theory which is a great start. Wheel re-invention prevented ... john.simmie[-]nuigalway.ie From owner-chemistry@ccl.net Fri Apr 6 08:45:01 2007 From: "Venkataramanan NS venkataramananns : gmail.com" To: CCL Subject: CCL: Jahn Teller distortion Message-Id: <-33986-070406014726-22024-hAPApsu2HjhdXL3qOsgJXA]_[server.ccl.net> X-Original-From: "Venkataramanan NS" Date: Fri, 6 Apr 2007 01:47:22 -0400 Sent to CCL by: "Venkataramanan NS" [venkataramananns*gmail.com] Dear viewers , Could someone suggest me to get convergence in the case of a Jahn Teller distortion system especially in the case of Ti(CO)6. I tried to increase the maxcyle, but it fails. Thanks in advance From owner-chemistry@ccl.net Fri Apr 6 09:20:00 2007 From: "Ashwini Bundhun ashwinibilly^^hotmail.com" To: CCL Subject: CCL: ts in gaussian Message-Id: <-33987-070406050346-26030-ypVT4zBISehoQe4g3/MdLQ|*|server.ccl.net> X-Original-From: "Ashwini Bundhun" Date: Fri, 6 Apr 2007 05:03:42 -0400 Sent to CCL by: "Ashwini Bundhun" [ashwinibilly:+:hotmail.com] Dear Alexsandra I think it is much easier to work with OPT=QST2. You may build the input file by using the command line, for example, p opt=qst2 freq=noraman b3lyp/6-31+g(d) geom=connectivity 1. Create an input file for the two reactants first (Hydrocarbon + OH). The problem here is that you must be able to guess the position of the OH radical, at such a distance that there will be a hydrogen abstraction from the hydrocarbon molecule. - (Reactant input file) 2. Open the first input file using the Gauss View, use the modify bond, remove the bond from the H atom connected to the hydrocarbon and thus forming a water molecule with the OH radical. Again here you must be able to guess the position of the water molecule to that of the new formed radical (Hydrocarbon). Save this file as a second input file. - (Products input file). (By using the reactants input file to create the products input file you will observe that the atoms will be in the same order). Note: geom=connectivity is important in both input files. 3. Open the Product input file, starting from the title line transfer the whole thing to the first input file, leaving one line from the last line. Using the same format of the command line as given above you should be able to view this single input file as containing the reacants and the products with Gaussview. Optimise the structures to search for a probable transition state. 4. Then use p opt=(CalcFc,TS) freq=noraman b3lyp/6-31+g(d) on the optimised structure. All the best, Ashwini Bundhun ashwinibilly:hotmail.com From owner-chemistry@ccl.net Fri Apr 6 09:59:01 2007 From: "liang wen lee liwl926===nenu.edu.cn" To: CCL Subject: CCL: analysis the band structure of TiO2 in Materials Studio Message-Id: <-33988-070405094932-21536-o/3LJNpzR+8/BpbyMYDK7A{=}server.ccl.net> X-Original-From: "liang wen lee" Date: Thu, 5 Apr 2007 09:49:18 -0400 Sent to CCL by: "liang wen lee" [liwl926 : nenu.edu.cn] 1.How can I get the band gap value from the -bandstructure.xcd file? 2.How can I identify which one is the Ti 3d band and which one is the O 2p band from -bandstructure.xcd file? From owner-chemistry@ccl.net Fri Apr 6 10:29:00 2007 From: "Gustavo Seabra gustavo.seabra|-|gmail.com" To: CCL Subject: CCL:G: Jahn Teller distortion Message-Id: <-33989-070406100442-17507-Sb7aPnax/jRoiP7aTAhYgg[-]server.ccl.net> X-Original-From: Gustavo Seabra Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 06 Apr 2007 10:04:24 -0400 MIME-Version: 1.0 Sent to CCL by: Gustavo Seabra [gustavo.seabra]_[gmail.com] Venkataramanan NS venkataramananns : gmail.com wrote: > Sent to CCL by: "Venkataramanan NS" [venkataramananns*gmail.com] > Dear viewers , > > Could someone suggest me to get convergence in the case of a Jahn Teller distortion system especially in the case of Ti(CO)6. I tried to increase the maxcyle, but it fails. > > Thanks in advance > This is just a guess, but I'd try to relax symmetry constraints in this case. If you use Gaussian, you can do that with NOSYMM. Gustavo. From owner-chemistry@ccl.net Fri Apr 6 11:04:01 2007 From: "dedey#alumni.bilkent.edu.tr" To: CCL Subject: CCL: significance of very small vibrational frequencies Message-Id: <-33990-070406095918-13595-VnuubneqKp0u71cLiWQJbA a server.ccl.net> X-Original-From: Date: Fri, 06 Apr 2007 16:00:40 EEST Sent to CCL by: [dedey#,#alumni.bilkent.edu.tr] Dear CCL members, My question is related with the significance of normal modes with very minor positive or negative frequencies. I do not doubt about considering a large molecule which has many -sort of- soft modes, due to rotations of groups like methyls,phenyls and so on, and exhibits frequencies on the order of -1 , -10 (cm-1) or simlar, as being a minimum. But avoiding such frequencies in optimizations may fail and what you end up becomes a TS mathematically. Tightening the convergence criteria, changing the optimization algorithms and playing with the step sizes may not help. I wonder if there is a published work -I could not manage to find- about the significance of very small negative frequencies,especially about semi empirical methods. If this is not present do you know about any published work which presents such structures as being a minimum and comments on the small negative frequencies as being insignificant or unimportant. Or what are your opinions about disregarding a vibration of about -1 , -10 cm-1 and declaring such a structure as a minimum. Thanks a lot... -- Yavuz Dede Comp. Chem. Lab. Dep. of Chem. METU 06531 Ankara TURKEY +90 312 210 3187 From owner-chemistry@ccl.net Fri Apr 6 11:39:01 2007 From: "Soren Eustis soren() jhu.edu" To: CCL Subject: CCL: Method for Frequency Calculations Message-Id: <-33991-070406111513-6104-fSfG2QvFy/lvDJnqLzkWdA:+:server.ccl.net> X-Original-From: "Soren Eustis" Content-language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 6 Apr 2007 11:15:00 -0400 MIME-Version: 1.0 Sent to CCL by: "Soren Eustis" [soren__jhu.edu] Disregarding any concerns with processor time and assuming extensive basis sets, what is generally accepted to be the most accurate method for frequency calculations of small (non-metallic) molecules? I have heard MP2 is not that great, but HF and DFT perform better? Am I on the right path here? From owner-chemistry@ccl.net Fri Apr 6 12:52:01 2007 From: "Arnab Chakrabarty r.arnab__gmail.com" To: CCL Subject: CCL: Material Studio issues Message-Id: <-33992-070406123655-25296-2Z2evf40bvRHciCvbCNepA]_[server.ccl.net> X-Original-From: Arnab Chakrabarty Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 06 Apr 2007 11:03:53 -0500 MIME-Version: 1.0 Sent to CCL by: Arnab Chakrabarty [r.arnab%gmail.com] Hi, I am not sure if this an appropriate topic to post in this group but i am having problems running Material Studio 4.0 in Windows Vista. I can build molecules but when i try minimizer, it pops up with problem regarding Gateway. In XP everything was fine. I would appreciate any inputs on this . Thanking in advance. Thanks Arnab From owner-chemistry@ccl.net Fri Apr 6 13:55:00 2007 From: "Emilio Xavier Esposito emilio.esposito*gmail.com" To: CCL Subject: CCL:G: gaussian error Message-Id: <-33993-070406120600-10586-WAblihHHRp0J61iRYD+s6w.:.server.ccl.net> X-Original-From: "Emilio Xavier Esposito" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 6 Apr 2007 11:06:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Emilio Xavier Esposito" [emilio.esposito],[gmail.com] Hi Sachin Your calculations are failing because of a 'Stale NSF file handle.' This is common when reading and writing your Gaussian scratch files to a network drive (NSF mounted) and the NSF server cannot keep up with the requests. The scratch files are written to the users home directory (or other location) on a NSF mount instead of to the node's local scratch directory (local hard drive). Storing your Gaussian files (input, output, and scratch) on the local hard drive of the initial compute node should fix this problem. All the best Emilio On 4/5/07, Sachin Tyagi sachintyagi1 ~~ gmail.com wrote: > > Sent to CCL by: "Sachin Tyagi" [sachintyagi1,+,gmail.com] > Hi I am trying to do some gaussian calculations but I am getting the following errors.... > > 1. Inv2: IOpt= 1 Iter= 1 AM= 3.04D-15 Conv= 1.00D-12. > Inverted reduced A of dimension 497 with in-core refinement. > Isotropic polarizability for W= 0.000000 155.14 Bohr**3. > End of Minotr Frequency-dependent properties file 721 does not exist. > fclose of exec file failed. > fclose of exec file failed.: Stale NFS file handle > > 2. Rotational constants (GHZ): 0.9383615 0.2268397 0.1971649 > Standard basis: 6-31G (6D, 7F) > There are 185 symmetry adapted basis functions of A symmetry. > Integral buffers will be 262144 words long. > Raffenetti 2 integral format. > Two-electron integral symmetry is turned on. > 185 basis functions, 459 primitive gaussians, 185 cartesian basis functions > 71 alpha electrons 71 beta electrons > nuclear repulsion energy 1420.4786747481 Hartrees. > NAtoms= 29 NActive= 29 NUniq= 29 SFac= 7.50D-01 NAtFMM= 320 NAOKFM=F Big=F > One-electron integrals computed using PRISM. > NBasis= 185 RedAO= T NBF= 185 > NBsUse= 185 1.00D-06 NBFU= 185 > read from file GXX-Exec.Dat failed > Returned from execl,istat=-1,errno=2! > Returned from execl! > > I wonder if somebody could help me in fixing the problems. > > Thanks > > sachin > From owner-chemistry@ccl.net Fri Apr 6 14:30:01 2007 From: "Herbert Fruchtl herbert.fruchtl]-[st-andrews.ac.uk" To: CCL Subject: CCL:G: ORCA and G03 Message-Id: <-33994-070406140214-26103-asPbM5nngXjsS4BM1QjWLQ^_^server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 06 Apr 2007 19:01:45 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl*_*st-andrews.ac.uk] Did anybody get the latest version of ORCA (2.5.20) to work with the G03 optimizer? If I set it up as described in the manual, Gaussian ends with: External calculation of energy, first and second derivatives. MO and density RWFs will be updated without deorthogonalization. Running external command "Gau_External R" input file "/users/hf63/ORCA_g03opt/h2o/Gau-23195.EIn" output file "/users/hf63/ORCA_g03opt/h2o/Gau-23195.EOu" Failed to open output file from external program. The first file (.EIn) exists, the second one (.EOu) doesn't. Thanks in advance, Herbert -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Fri Apr 6 15:05:01 2007 From: "kcousins]![csusb.edu" To: CCL Subject: CCL: Animation of alpha helix wanted Message-Id: <-33995-070406112218-11329-hiR/g/PxkWBPXW6a1qx+Gg_+_server.ccl.net> X-Original-From: kcousins^csusb.edu Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Fri, 06 Apr 2007 07:38:35 -0700 MIME-version: 1.0 Sent to CCL by: kcousins^^csusb.edu Ttry this: http://atlas.riken.go.jp/mdm/movies.html Kimberley R. Cousins Professor of Chemistry California State University, San Bernardino http://chem.csusb.edu/~kcousins kcousins]=[csusb.edu ----- Original Message ----- > From: "Josef Scheiber mail|a|josef-scheiber.de" Date: Thursday, April 5, 2007 10:29 pm Subject: CCL: Animation of alpha helix wanted To: "Cousins, Kimberley " > > Sent to CCL by: Josef Scheiber [mail|josef-scheiber.de] > Hi Don, > > maybe this can help you: > http://www-cgi.uni- > regensburg.de/Klinik/FunktionelleGenomik/Compdiag/structure/fold.html > Best, Sepp > > Donald J. Keidel keided01:ucr.edu wrote: > > Sent to CCL by: "Donald J. Keidel" [keided01**ucr.edu] > > > > I am looking for an animation that someone might have or know > whwere to > > download that shows a protein going from primary structure to > alpha helix. > > I wanted to use it in my course to illustrate how the hydrogen > bonding> pattern develops. I have searched the net with no luck. > Thank you in > > advance for all suggestions. > > > > Don Keidel> > > > > > > > > -= 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 Apr 6 15:40:01 2007 From: "Green Power powergreen-*-gmail.com" To: CCL Subject: CCL: Integral cutoff Message-Id: <-33996-070406061644-31548-UNz+KR17sMLIntVQnihedw-$-server.ccl.net> X-Original-From: "Green Power" Content-Type: multipart/alternative; boundary="----=_Part_3109_12721113.1175851034073" Date: Fri, 6 Apr 2007 05:17:14 -0400 MIME-Version: 1.0 Sent to CCL by: "Green Power" [powergreen _ gmail.com] ------=_Part_3109_12721113.1175851034073 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, All, Is there any way to turn off one and two electron integrals involved with remote atom sites during a SCF process, for example as following, C1--C2--C3--C4--C5, I want to make the Fork matrix element F15=0, so as to remove the direct interact between C1 and C5. Any suggestion will be highly appreciated. Tian ------=_Part_3109_12721113.1175851034073 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, All,

Is there any way to turn off one and two electron integrals involved with remote atom sites during a SCF process, for example as following,

C1--C2--C3--C4--C5,

I want to make the Fork matrix element F15=0, so as to remove the direct interact between C1 and C5.
Any suggestion will be highly appreciated.

Tian

------=_Part_3109_12721113.1175851034073-- From owner-chemistry@ccl.net Fri Apr 6 19:58:01 2007 From: "Abrash, Samuel sabrash^^^richmond.edu" To: CCL Subject: CCL:G: Method for Frequency Calculations Message-Id: <-33997-070406153550-20278-cXrf0+yYosJwJg32kxlvPQ^_^server.ccl.net> X-Original-From: "Abrash, Samuel" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Fri, 6 Apr 2007 12:57:15 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Samuel" [sabrash(-)richmond.edu] If you choose a DFT Method with a biggish basis set, you can get within a few % of literature values. People who do matrix isolation spectroscopy and commonly use Gaussian for vibrational spectrum calculations usually use B3LYP/6-311++G**. You can also get a sense of the accuracy by going to CCCBDB and going to scaling factors. The closer the scaling factor is to one for a combination of theory and basis set, the more accurate it is. HF performs worse than MP2 as far as absolute frequencies go, but tends to have frequency patterns that match experiment better. MP2 gives smaller scaling factors but can be unpredictable regarding whether frequencies are over or underestimated. Best regards, Sam Abrash Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash#%#richmond.edu Web-page: http://oncampus.richmond.edu/~sabrash "Rabbi Yitzhak said: At the time God created the world and desired to reveal the depth of His being from out of the hidden, the light came > from the darkness and they were joined together. Because of this, out of darkness came the light and out of the hidden came the revealed and out of the good came evil and out of mercy came severe judgement, and everything is intertwined with everything else...the good inclination and the evil inclination, the right and the left." - The Zohar -----Original Message----- > From: owner-chemistry#%#ccl.net [mailto:owner-chemistry#%#ccl.net] Sent: Friday, April 06, 2007 11:15 AM To: Abrash, Samuel Subject: CCL: Method for Frequency Calculations Sent to CCL by: "Soren Eustis" [soren__jhu.edu] Disregarding any concerns with processor time and assuming extensive basis sets, what is generally accepted to be the most accurate method for frequency calculations of small (non-metallic) molecules? I have heard MP2 is not that great, but HF and DFT perform better? Am I on the right path here?http://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 Fri Apr 6 20:33:01 2007 From: "Amandeep kaur Sangha aksangha^_^bu.edu" To: CCL Subject: CCL: Coarse-graining a Non-Markov process to a Markov process Message-Id: <-33998-070406191058-4260-v/4Cna/TB11siM7Ukq+0lg::server.ccl.net> X-Original-From: Amandeep kaur Sangha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 6 Apr 2007 18:39:17 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Amandeep kaur Sangha [aksangha-$-bu.edu] Hello Folks, I am trying to study dynamics of protein folding. For that i have to turn this non-markov process of folding to a markov process. I am doing both spatial and temporal coarse-graining. To my knowledge, there are three tests i can do to check if i m successful to obtain a markov process after coarse-graining. 1. Eigenvalue analysis of Transition probability matrix 2. Life time distribution of states of the system 3. History dependent transitions among various states of the system I do coarse-graining with one set of space and time parameters and check if the eigenvalues decay is exponential(which means process is markov). But i could not get markov process even for larger times for temporal coarse-graining at any parameter used for spatial coarse- graining. I mean, i could not see eigenvalues decaying exponentially. May be because the process has not necessarily turned into a markov ( i mean 100%). My question is, IS there any sound way to know what space and time parameter should i use for coarse-graining such that i get markov process?? OR If i keep on increasing the time parameter, where should i stop?? Is there any check for that? and How actually i can check for histroy dependent transitions on the way from non-markov to markov process?? becasue no history dependent transitions means markov process. Any suggestions are welcome ! amandeep. aksangha(-at-)bu.edu From owner-chemistry@ccl.net Fri Apr 6 22:08:01 2007 From: "Wayne Steinmetz WES04747^pomona.edu" To: CCL Subject: CCL: qsar volume calculation using hyperchem/other software Message-Id: <-33999-070405195449-21487-rFdwrv37CCmUMecNbYd9AQ-$-server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Apr 2007 16:22:16 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747!^!pomona.edu] I use SYBYL for this type of project. SYBYL provides a wide array of modules, its own spreadsheet, and its own very flexible programming language. I shudder at the task of merging Hyperchem output with Micro#### products. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz.-$-.pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry.-$-.ccl.net [mailto:owner-chemistry.-$-.ccl.net] Sent: Thursday, April 05, 2007 12:12 PM To: Wayne Steinmetz Subject: CCL: qsar volume calculation using hyperchem/other software Sent to CCL by: "Shivani Syal" [ssyal[-]purdue.edu] Hi everyone, I'm trying to write an excel macro/hcl script to automate solvent-excluded volume calculations using hyperchem but I'm having errors running it. Hperchem is not executing simple commands like 'qsar-property volume' using either DDE (via excel) or hcl scripts. In short, it is opening the dialog box but not changing the default option and performing the calculation. Does anyone have experience with a similar issue or know if such a functionality (doing batch calculations using the qsar module) is even possible in hyperchem? If not, can someone recommend a reliable software/program which gives the flexibility of computing volumes for different probe radii.(I'm not posting my script here for brevity reasons, but would be glad to do do if someone has any experience with the same). Thanks, Shivanihttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software.