From owner-chemistry@ccl.net Thu Dec 20 02:05:01 2007 From: "Andreas Klamt klamt=-=cosmologic.de" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35888-071220020126-29532-98BATifLAWO6+3brC2uz7g#server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 20 Dec 2007 08:01:11 +0100 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt:+:cosmologic.de] Hi Dave, this is an unusual CCL_entry! Anyway, if you like to have something really novel and different in your suite, try our COSMOtherm/COSMOfrag suite for ADME properties, pKa, drug similarity and much more. We probably have the most fundamental and ab initio (but still slightly fitted) approach to these properties. It is based on quantum chemistry combined with the COSMO-RS fluid phase thermodynamics. High-Throughput screening is enabled by COSMOfrag, which avoids the DFT/COSMO caclualtions for the individual compounds by taking the information from precalculated fragments of ~50000 druglike compounds. COSMOfrag/COSMOtherm runs ~5 compounds per second on a standard CPU. Best regards Andreas Dave . ccl_list~~giantscience.com schrieb: > Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] > I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. > > The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. > > The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? > > I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. > > Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. > > I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.> > > > > -- ----------------------------------------------------------------------------- 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 Dec 20 03:17:00 2007 From: "Philippe Carbonniere philippe.carbonniere[]univ-pau.fr" To: CCL Subject: CCL:G: "Low frequencies" in Gaussian Freq Jobs Message-Id: <-35889-071219123617-1908-cISwCrpdtj1+sFWQsg6kXg-x-server.ccl.net> X-Original-From: Philippe Carbonniere Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 19 Dec 2007 17:35:56 +0100 MIME-Version: 1.0 Sent to CCL by: Philippe Carbonniere [philippe.carbonniere],[univ-pau.fr] Dear Andrea, Pay attention to use opt=3Dtight (but maybe this is the default for this = kind of calculations) and if you use DFT : int=3Dgrid=3Dultrafine. You wi= ll=20 lower the six eigenvalues corresponding to rotation and translation. Concerning the common range of this values I would say between -5 and=20 +(5-10) cm-1 for organic systems. Maybe this changes for inorganic=20 systems (who knows !) but I have no experience on that systems. Hopping this will be help you, Philippe Carbonniere Andrea Ciccioli andrea.ciccioli+*+uniroma1.it a =E9crit : >Sent to CCL by: "Andrea Ciccioli" [andrea.ciccioli_-_uniroma1.it] >Dear friends, > >it is commonly asserted in textbooks and software manuals that the obvio= us test to recognize minima in PES among stationary points is that the vi= brational frequencies have to be real. >However, I wonder if besides this criterium one should also check carefu= lly the values of the frequencies reported as "Low frequencies" in Gaussi= an outputs (just before the list of Harmonic frequencies). These are the = "frequencies" actually corresponding to translations and rotations, and t= hey should be ideally equal to zero, and indeed in many cases they are ve= ry low. However, it happens not seldom to me, e.g. for triatomic species = containing heavy elements such as transition metals, to obtain outputs wh= ere, although the harmonic vibrational frequencies are all real (positive= numbers in the Gaussian output), ie the structure should be a minimum, n= evertheless one or two "Low Frequencies" are not that low. Furthermore, t= hey are in general both positive and negative. For example, low frequenci= es as high as +/- 10 to 40 cm-1 are obtained. Moreover, these values are= apparently larger for analytic second-derivative frequency calculations = than for numerical calculations (I use DF! > T methods). >As far as you know, these relatively high values of the "Low Frequencies= " can indicate that the calculated structure is not a true minimum, in sp= ite of having real harmonic frequencies ? What could be a reasonable crit= erium to consider the "Low frequencies" small enough to be sure that the = stationary point is a true minimum ? >Has anyone some suggestions/indications to give me ? >Thanks to all, and season's greetings. >Andrea Ciccioli >University of Rome (ITALY) >Sapienza > > > >-=3D This is automatically added to each message by the mailing script =3D= -=> >Subscribe/Unsubscribe:=20> >Job: http://www.ccl.net/jobs=20> >Search Messages: http://www.ccl.net/htdig (login: ccl, Password: search= )> > > > =20 > From owner-chemistry@ccl.net Thu Dec 20 05:04:01 2007 From: "Herbert Fruchtl herbert.fruchtl[a]st-andrews.ac.uk" To: CCL Subject: CCL:G: Problems finding TS Message-Id: <-35890-071220050102-15884-qg7wiMGDx65Y0TFj817OWw=-=server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Dec 2007 10:00:19 +0000 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl],[st-andrews.ac.uk] What I usually do in this case: - Guess the length of the bond at the TS, or look for the maximum in a relaxed PES scan. - Optimize to a minimum with this bond frozen at this value. - Start TS search from this point. If possible, calculate a Hessian (with a smaller basis and a pure DFT functional like HCTH or BLYP) You have ModRedundant AND TS in your input. I don't know what you're freezing, but this won't give you a true TS. Also, if you are so far off that you need NoEigenTest, it's unlikely you find the correct TS. Herbert Debellis Anthony CE US anthony.debellis,,ciba.com wrote: > Sent to CCL by: Debellis Anthony CE US [anthony.debellisHello Oscar, > One possibility would be to locate the transition state with the methyl group removed, then add back the methyl to the resulting TS structure followed by a further TS optimization. > Anthony DeBellis > Ciba > > -----Original Message----- >> From: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net] > Sent: Tuesday, December 18, 2007 12:05 PM > To: Debellis Anthony CE US > Subject: CCL:G: Problems finding TS > > > Sent to CCL by: Oscar Odio Chacón [odio---imre.oc.uh.cu] > > Hello, CCLers: > I´m trying to calculate the transition state of a radical addition reaction to an olefin using Gaussian 98. The problem arises because the output negative frequency does not correspond with vibrational motion of the bond formed in the product, but corresponds to a motion associated with a methyl group near the radical. So, what can I do? > Remove the methyl group? > In my opinion, this methyl group would have influence in the transition state energy. > The overall system contains 47 atoms, 415 basis functions, 707 primitive gaussians, 70 alpha electrons, 69 beta electrons. The command line was # > b3lyp/6-31g(d,p) opt=(modredundant, TS, noeigentest) freq. > Thanks in advance. > Oscar Odio > > > > > > -- > Lic. Oscar Odio Chacón > Laboratorio de Polímeros > IMRE > > > > "Al mundo nuevo corresponde la Universidad nueva" > UNIVERSIDAD DE LA HABANA > 280 aniversario > Participe en Universidad 2008 del 11 al 15 de febrero del 2008. > Palacio de Convenciones. La Habana. Cuba. > http://www.universidad2008.cuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > -> > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Thu Dec 20 08:20:01 2007 From: "nand kishor gour gour_nand_+_rediffmail.com" To: CCL Subject: CCL: Computational Chemistry Message-Id: <-35891-071220022638-6885-8bfiS8nOZVYQF0AvdkhSyA/./server.ccl.net> X-Original-From: "nand kishor gour" Date: Thu, 20 Dec 2007 02:26:34 -0500 Sent to CCL by: "nand kishor gour" [gour_nand[A]rediffmail.com] i m finding transtion state in the isomerization reaction between allene to propyne using QST2 methods but every time link is died. i m doing caculation using HF/6-31g(d)and additional keywords opt=noeigentest. Nand Kishor Gour gour_nand * rediffmail.com From owner-chemistry@ccl.net Thu Dec 20 09:13:01 2007 From: "aa aa.\a/.chemaxon.hu" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35892-071220082727-5717-nZvo4YgxuPBLulvEAcQ1hQ\a/server.ccl.net> X-Original-From: aa Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Dec 2007 07:41:32 -0500 MIME-Version: 1.0 Sent to CCL by: aa [aa/a\chemaxon.hu] HI Dave, I can't help with spending your budget but I would point at the ChemAxon products, they are Java based cheminformatics toolkits and desktop applications and all are free for academic use. There are connection nodes for Pipeline Pilot and the I am sure there will be something(s) in the range that is relevant (visualization, search, property calculation, clustering, fragmentation, 2D/3D screening and core informatics platform build etc). I think this page (http://www.chemaxon.com/products.html) and the links there are the best start point to see what we have that might be useful, here is a list of current Academic Package subscribers (http://www.chemaxon.com/apl/index_i.html), our UGM presentations may be useful to see what the industry is doing with us (http://www.chemaxon.com/UGM/ugm_land.html) and perhaps this listing (http://www.chemaxon.com/forum/forum28.html) of public implementations could also give ideas. To see the conditions and sign up for Academic Package please visit this link (http://www.chemaxon.com/acpack_conditions.html) - you will need an existing forum registration (http://www.chemaxon.com/forum/profile.php) to apply. If I can help your understanding let me know - I am just over the river. Best regards of the season (as the snow falls this morning in Brookline) Alex Dave . ccl_list~~giantscience.com wrote: > Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] > I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. > > The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. > > The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? > > I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. > > Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. > > I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.> > > From owner-chemistry@ccl.net Thu Dec 20 14:00:00 2007 From: "Steve Bowlus chezbowlus||comcast.net" To: CCL Subject: CCL:G: Problems finding TS Message-Id: <-35893-071220103044-27717-KFVCTcC3yMw1iONrmBIlNw * server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Dec 2007 07:30:12 -0800 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus-x-comcast.net] Alternatively, the mode identified as the reaction coordinate may be that of rotation of the methyl group, and the TS identified is where eclipsing interactions are maximized. This is a common problem; try resetting the methyl dihedrals well away from any eclipsed (or other close-approach conformation), and reoptimize the TS. Steve Bowlus Debellis Anthony CE US anthony.debellis,,ciba.com wrote: > Sent to CCL by: Debellis Anthony CE US [anthony.debellis=ciba.com] > Hello Oscar, > One possibility would be to locate the transition state with the methyl group removed, then add back the methyl to the resulting TS structure followed by a further TS optimization. > Anthony DeBellis > Ciba > > -----Original Message----- > >>From: owner-chemistry^^ccl.net [mailto:owner-chemistry^^ccl.net] > > Sent: Tuesday, December 18, 2007 12:05 PM > To: Debellis Anthony CE US > Subject: CCL:G: Problems finding TS > > > Sent to CCL by: Oscar Odio Chacón [odio---imre.oc.uh.cu] > > Hello, CCLers: > I´m trying to calculate the transition state of a radical addition reaction to an olefin using Gaussian 98. The problem arises because the output negative frequency does not correspond with vibrational motion of the bond formed in the product, but corresponds to a motion associated with a methyl group near the radical. So, what can I do? > Remove the methyl group? > In my opinion, this methyl group would have influence in the transition state energy. > The overall system contains 47 atoms, 415 basis functions, 707 primitive gaussians, 70 alpha electrons, 69 beta electrons. The command line was # > b3lyp/6-31g(d,p) opt=(modredundant, TS, noeigentest) freq. > Thanks in advance. > Oscar Odio > > > > > > -- > Lic. Oscar Odio Chacón > Laboratorio de Polímeros > IMRE > > > > "Al mundo nuevo corresponde la Universidad nueva" > UNIVERSIDAD DE LA HABANA > 280 aniversario > Participe en Universidad 2008 del 11 al 15 de febrero del 2008. > Palacio de Convenciones. La Habana. Cuba. > http://www.universidad2008.cuhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/spammers.txt > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Thu Dec 20 14:35:00 2007 From: "Darryl Reid darryl.reid ~ gmail.com" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35894-071220124036-10874-+D1IAzVPPgWw3z0cvnJZMg++server.ccl.net> X-Original-From: "Darryl Reid" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 Dec 2007 11:44:12 -0500 MIME-Version: 1.0 Sent to CCL by: "Darryl Reid" [darryl.reid]*[gmail.com] Hi Dave, First off, it sounds like you will have a good array of software in place with MOE, Pipeline Pilot, etc. However, I do encourage you to look at some of the "free for academic" options. For docking and ligand-based screening, we (SimBioSys) offer both eHiTS and LASSO for academic research and teaching. We also have CheVi for visualization. For more 2D / 1D stuff, I would suggest looking at the ChemAxon or ACD/Labs stuff. Feel free to contact me if you want to talk about this in detail. Regards, Darryl www.simbiosys.ca On Dec 19, 2007 1:29 PM, Dave . ccl_list~~giantscience.com wrote: > > Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] > I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. > > The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. > > The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? > > I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. > > Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. > > I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.> > > From owner-chemistry@ccl.net Thu Dec 20 15:15:01 2007 From: "Andrew Orry andy^_^molsoft.com" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35895-071220150022-5347-fs3ipYqnN9UkmsREV0phLg],[server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 20 Dec 2007 11:38:24 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [andy- -molsoft.com] Dave, An opportunity like this on CCL does not come up very often so I will make the most of it! Please consider the MolSoft ICM (www.molsoft.com) suite of computational chemistry and biology software. ICM-Pro is our main desktop modeling program and contains all the essential tools for structure based drug design in one easy to use package and interface (available for Windows, Mac, SGI and Linux). The main features of MolSoft's ICM software are: PDB structure and sequence analysis, a dynamically linked alignment to 3D structure environment, molecular modeling and structure optimization, crystallographic tools (electron density map visualization and fitting tools, BIOMT molecule generation, symmetry related molecules), structure quality control tools, small molecule and protein-protein docking, virtual screening and scoring, flexible ligand-receptor docking, and a comprehensive suite of cheminformatics tools including chemical/pharmacophore searching, ADME analysis, focused library development, Markush enumeration, chemical superposition and clustering (see: http://www.molsoft.com/chemistry.html). ICM-Pro is also a great tool for communicating data with your colleagues in the lab via MolSoft's Molecular Documents and Presentation technology (for an example, see how the Structural Genomics Consortium at Oxford University use ICM to present their data here http://www.sgc.ox.ac.uk/iSee/downloads.html). The ICM-Browser (http://www.molsoft.com/icm_browser.html) is a free download and can be used to view these files. If you have any questions or would like a trial version please let me know. Thanks, Andy 858 625 2000 (x108) -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com Dave . ccl_list~~giantscience.com wrote: > Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] > I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. > > The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. > > The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? > > I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. > > Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. > > I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.> > -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From owner-chemistry@ccl.net Thu Dec 20 15:45:00 2007 From: "Dipesh Risal drisal##accelrys.com" To: CCL Subject: CCL: Setting up new (academic) research lab; software purchase questions Message-Id: <-35896-071220143906-21046-wfj7sD7Fi0lDGmsq44M44g[]server.ccl.net> X-Original-From: Dipesh Risal Content-Type: multipart/alternative; boundary="=_alternative 0067C46B882573B7_=" Date: Thu, 20 Dec 2007 10:53:23 -0800 MIME-Version: 1.0 Sent to CCL by: Dipesh Risal [drisal#accelrys.com] This is a multipart message in MIME format. --=_alternative 0067C46B882573B7_= Content-Type: text/plain; charset="US-ASCII" Hi Dave, We are very concerned that you heard we are not friendly to academics :-) As you mentioned PipelinePilot from Accelrys is available for free! (http://www.accelrys.com/products/scitegic/pp-student/) We are encouraging academic users to use this resource to create scientific software applications, integrate their scientific code, and share their innovations with the general Pipeline Pilot community. Just to quash the rumors, our academic pricing for all software is very competitive & I believe you have already been contacted in this regard by our Academic team. If not, please feel free to get in touch with me and we can discuss this off-line. Sincerely, Dipesh Risal, Ph. D. Product Manager, Life Sciences Accelrys, Inc. 10188 Telesis Court, Suite 100 San Diego, CA 92121, U.S.A. Tel: +1 (858) 799 5224, Cell: +1 (858) 414 2702 Fax: +1 (858) 799 5100 email: drisal!=!accelrys.com http://www.accelrys.com "Dave . ccl_list~~giantscience.com" Sent by: owner-chemistry!=!ccl.net 12/19/2007 10:29 AM Please respond to "CCL Subscribers" To "Risal, Dipesh " cc Subject CCL: Setting up new (academic) research lab; software purchase questions Sent to CCL by: "Dave ." [ccl_list,,giantscience.com] I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening. The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite. The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable? I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly. Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger. I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Click on the link below to report this email as spam https://www.mailcontrol.com/sr/3pgq029XLUHBsyz1eL5mU3bBEH+k1scvHtOocGAKmxEoqI5kcj8OWTA1r6DIS5xxXBpcuIqf1kISoVpGO9S6FHhRyt7GrGEZpsrxUBDUox3O4AKCvM6TTLGMv58IKG2+LztAWC2xm7mOnwqLlNHtMEQeJeqmLtKY9A+IZt4stbT7A3haPhCrEkK0KQ+kBNVw6rqb4BXWsuhhIOg393TAyk9u!n4UIOoj --=_alternative 0067C46B882573B7_= Content-Type: text/html; charset="US-ASCII"
Hi Dave,

We are very concerned that you heard we are not friendly to academics :-)
As you mentioned PipelinePilot from Accelrys is available for free! (http://www.accelrys.com/products/scitegic/pp-student/)
We are encouraging academic users to use this resource to create scientific software applications, integrate their scientific code, and share their innovations with the general Pipeline Pilot community.

Just to quash the rumors, our academic pricing for all software is very competitive & I believe you have already been contacted in this regard by our Academic team.
If not, please feel free to get in touch with me and we can discuss this off-line.

Sincerely,

Dipesh Risal, Ph. D.
Product Manager, Life Sciences
Accelrys, Inc.
10188 Telesis Court, Suite 100
San Diego, CA 92121, U.S.A.
Tel:  +1 (858) 799 5224, Cell:  +1 (858) 414 2702
Fax: +1 (858) 799 5100
email: drisal!=!accelrys.com
http://www.accelrys.com


"Dave . ccl_list~~giantscience.com" <owner-chemistry!=!ccl.net>
Sent by: owner-chemistry!=!ccl.net

12/19/2007 10:29 AM
Please respond to
"CCL Subscribers" <chemistry!=!ccl.net>
To
"Risal, Dipesh " <drisal!=!accelrys.com>
cc
Subject
CCL: Setting up new (academic) research lab; software purchase questions






Sent to CCL by: "Dave  ." [ccl_list,,giantscience.com]
I'm in the process of setting up a new modeling research lab at MIT (academic lab). I'm trying to put together a budget for modeling software we'll want to purchase for the coming year. We will be part of a drug design effort, so we'll be doing the standard stuff associated with such an effort (visualization of ligands and proteins, docking, scoring [binding, ADME], etc.) We expect to have a lot of compounds/data flowing through via library screening.

The software we already have access to (free to us) includes the MOE package, Pipeline Pilot, and the complete CambridgeSoft suite.

The question is: What software should I budget purchasing? I was considering, in particular, the Schrodinger stuff. The quote I got was $11,500/year for a single license for their suite, or $5000/year for 20 "tokens", that will allow me to run run 3-4 of their programs simultaneously. Any suggestions/comments on this pricing and which option is preferable?

I'd like to bring in Insight, because that's the program I've used for visualization for a long time, but I've heard that Accelrys' pricing is not too academic friendly.

Alternatively, I can bring in the academic (nearly) freeware: Amber, Dock, Modeler, PyMol, etc. Of course, then you don't get the nice(r) integration of stuff like Schrodinger.

I'm open to hearing alternatives, yes/nos, etc. We can definitely put money in the budget for modeling software. I just don't want to toss money into the street unnecessarily.


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--=_alternative 0067C46B882573B7_=-- From owner-chemistry@ccl.net Thu Dec 20 20:56:01 2007 From: "N Venkataramanan S venkataramananns!=!gmail.com" To: CCL Subject: CCL: reactant complex Message-Id: <-35897-071220205359-6950-zwkDwrlmTdzbO2VyndkGsA]|[server.ccl.net> X-Original-From: "N Venkataramanan S" Date: Thu, 20 Dec 2007 20:53:56 -0500 Sent to CCL by: "N Venkataramanan S" [venkataramananns() gmail.com] Dear CCL users I am trying to optmize a structure involving a reactant complex (Fe (OXO) complex + Organic substrate). When i try to optimize the system with opt keyword the organic substrate keeps on moving from initial distance of 2.5 to 13 without converging(even after 75 opt cycles). When using opt=(TS) the same problem occurs. In liteature, I saw some reports on similar systems that the distance between the oxo and hydrogen of the substrates were about 2 to 2.5 (references : J. Phys. Chem. C 2007, 111, 12397-12406, J. Am. Chem. Soc. 2006, 128, 8590-8606) Please suggest me some method to shortout the problem. With thanks in advance Sincerely Venkataramanan From owner-chemistry@ccl.net Thu Dec 20 23:33:00 2007 From: "Naser Eltaher Eltayeb nasertaha90 : yahoo.co.uk" To: CCL Subject: CCL:G: DecCub-RdMo error Message-Id: <-35898-071220232901-8860-1dQQruvhX9oH8YpCgNXf7Q^-^server.ccl.net> X-Original-From: "Naser Eltaher Eltayeb" Date: Thu, 20 Dec 2007 23:28:57 -0500 Sent to CCL by: "Naser Eltaher Eltayeb" [nasertaha90 _ yahoo.co.uk] Dear All I am using G 03, I am trying to visullize HOMO and LUMO orbitals, after I generate molecular orbital and save it as .chk, then I get the error message below "Running Cubegen Series Job... Executing Gaussian Cubegen => C:\G03W\cubegen.exe 0 mo=174 "C:\G03W\Scratch\gv-1374\rjvjv.fch" "C:\G03W\Scratch\gv-1374\00lx26.cub" -2 h Out-of-memory error in routine DecCub-RdMO (IEnd= 10310160 MxCore= 6290325) Use %mem=10MW to provide the minimum amount of memory required to complete this step. Error termination via Lnk1e at Fri Dec 21 12:27:21 2007. Cubegen Job Completed (PID = 1f50, status = 2057) Cubegen Series Job Completed" Could anybody help me to solve this problem Thank you Naser Eltaher