From owner-chemistry@ccl.net Tue Mar 11 05:10:01 2008 From: "Pascal Boulet pascal.boulet-,-univ-provence.fr" To: CCL Subject: CCL: How to model force field of metal carbide with the help of ab initio d Message-Id: <-36474-080311043502-8079-yFp4oqOFGPa1RbDFWoey0A\a/server.ccl.net> X-Original-From: Pascal Boulet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Mar 2008 09:03:25 +0100 MIME-Version: 1.0 Sent to CCL by: Pascal Boulet [pascal.boulet**univ-provence.fr] Hello, I know that there are FF for metals in the GULP program. In addition, Tersoff and Brenner developped a FF (EAM: embedded atom model) to model metal-metal interactions. It also includes interactions with carbon. Hope this help Best Regards Pascal Utpal Sarkar utpalchemiitkgp : gmail.com wrote: > Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp-.-gmail.com] > Hi CCL Users: > I am doing the molecular dynamics simulation of metal carbide. But I couldnot find suitable force field of metal( Fe, Co, Ni etc) carbide. So I am trying to model the force field with the help of ab initio calculation. But I donot have any idea how to do it practically. > Does anybody help me formulating the force fied for it? > Any kind of help is greately appreciable. > Thanks and regards > Utpal Sarkar> > > -- Dr. Pascal Boulet, Computational Chemist University of Provence Laboratoire Chimie Provence, UMR6264 Centre Saint-Jerome, case MADIREL F-13397 MARSEILLE Cedex 20, France Tel. +33 (0) 491 63 71 17 Fax. +33 (0) 491 63 71 11 courriel: pascal.boulet{:}univ-provence.fr http://www.lc-provence.fr http://allos.up.univ-mrs.fr/boulet From owner-chemistry@ccl.net Tue Mar 11 09:09:01 2008 From: "Kanchana Thanthiriwatte kst25~~msstate.edu" To: CCL Subject: CCL:G: G03:hyperpolarizability calculations Message-Id: <-36475-080310130454-11674-bW6JjoDBkj5OLFDO+W9qJQ###server.ccl.net> X-Original-From: Kanchana Thanthiriwatte Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 10 Mar 2008 10:55:32 -0500 MIME-Version: 1.0 Sent to CCL by: Kanchana Thanthiriwatte [kst25.:.msstate.edu] Hi soumya, you can refer following paper. Thanthiriwatte, K. S. et. al. J. Mol. Struct. (Theochem)2002, v617, pp169-175 It had full discretion for calculating hyperpolarizabilities. If you can not find this paper just let me know. Good luck. Regards, -Kanchana- /*---------------------------*/ Kanchana S. Thanthiriwatte Department of Chemistry and HPCC Center for Computational Sciences, Mississippi State University Box 9573 Mississippi State, MS 39762 (Tel) 662-325-4633 (Fax) 662-325-1618 soumya samineni soumya_samineni%%rediffmail.com wrote: > Sent to CCL by: "soumya samineni" [soumya_samineni.,+,.rediffmail.com] > Hi all, > Sry for a naive question ... How can i get the hyperpolarizability of organic molecule using the G03 program ... > > thanx in advance > soumya> > From owner-chemistry@ccl.net Tue Mar 11 09:44:01 2008 From: "xiao hong zhao zhaoxiaohong1237{}sina.com" To: CCL Subject: CCL: Help :problems in excited states calculation of Ag4 using ADF Message-Id: <-36476-080311024611-23138-OLfRVEHICHvqUaqqvdvRCA()server.ccl.net> X-Original-From: "xiao hong zhao" Date: Tue, 11 Mar 2008 02:46:07 -0400 Sent to CCL by: "xiao hong zhao" [zhaoxiaohong1237/a\sina.com] Dear: An error Error in scfrho: fractional occupation numbers have not yet been implemented ! occurred when I calculated excitation states of an Ag4 molecule of Td geometry, while the other modules are normal. I have read the user-guider carefully and tried some ways, but I can't designate occupation number. Would you tell me what may induce this error in ADF? How could I solve this problem Thank you so much. Best wishes, From owner-chemistry@ccl.net Tue Mar 11 11:56:00 2008 From: "andras.borosy_+_givaudan.com" To: CCL Subject: CCL: 3D data visualisation software Message-Id: <-36477-080311114644-4056-01oVeqSoSNbIAB1nv049yg_-_server.ccl.net> X-Original-From: andras.borosy{=}givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 004E1D21C1257409_=" Date: Tue, 11 Mar 2008 15:16:08 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy-$-givaudan.com This is a multipart message in MIME format. --=_alternative 004E1D21C1257409_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, I would need simple and cheap 3D data visualisation software (in ideal=20 case an add in for Excel) like XLSAT 3D Plot ( http://www.modeladvisor.com/specific=5Fuse/others/statistic=5Fforecast/xlst= at=5F3dplot/xlstat=5F3dplot.htm ).=20 Might you suggest me anything? Many thank, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com --=_alternative 004E1D21C1257409_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,

I would need simple and ch= eap 3D data  visualisation software (in ideal case an add in for Excel) like XLSAT 3D Plot (http://www.modeladvisor.com/specific=5Fuse/others/stati= stic=5Fforecast/xlstat=5F3dplot/xlstat=5F3dplot.htm).

Might you suggest me anything?

Many thank,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-44-824 2164  -  F:+41-44-8242926    -  http:= //www.givaudan.com --=_alternative 004E1D21C1257409_=-- From owner-chemistry@ccl.net Tue Mar 11 12:35:01 2008 From: "Yujie Sun sun.205+/-osu.edu" To: CCL Subject: CCL:G: Problems of CIS optimization for excited states Message-Id: <-36478-080311110535-29872-HSousDVu3R/KX8CEMIoTbA^^server.ccl.net> X-Original-From: "Yujie Sun" Date: Tue, 11 Mar 2008 11:05:32 -0400 Sent to CCL by: "Yujie Sun" [sun.205]=[osu.edu] Hi CCLers, I am trying to calculate the first three triplet excited states of a ruthenium compound in acetonitrile via CIS method, followed by the optimization of the lowest excited state with the same method. Here is my input file. %chk=Ru-cis.chk %nproc=8 %mem=8GB #P cis=triplets scrf=(solvent=acetonitrile,cpcm) gen pseudo=read test Ru-ACN-cis 2 1 Cartesian Coordinates 6-31G* **** Ru 0 SDD **** Ru 0 SDD --Link1-- %chk=Ru-ACN-cis.chk %nproc=8 %mem=8GB #P ucis(root=1,read) scrf=(solvent=acetonitrile,cpcm) gen pseudo=read opt=gdiis freq geom=check guess=read test Ru-ACN-Ex 2 3 H C N 0 6-31G* **** Ru 0 SDD **** Ru 0 SDD The first job can be completed successfully, however for the second job I always encounter this error message: Restoring guess from checkpoint file densities. Density file must contain transition densities. Error termination via Lnk1e in /usr/local/g03d01/g03/l914.exe at Tue Mar 11 01:40:32 2008. Does anybody have some clues about this problem? What does "density file must contain transition densities" mean? Do I need to add "density=all" in my second job route section? Or any other suggestions? Thanks a lot in advance. Best regards, Yujie sun.205,+,osu.edu From owner-chemistry@ccl.net Tue Mar 11 13:06:01 2008 From: "Otello Maria Roscioni omr^^soton.ac.uk" To: CCL Subject: CCL: building a nanoparticle Message-Id: <-36479-080311115515-5485-oeEqXTleQjruy5Zunf97dA . server.ccl.net> X-Original-From: Otello Maria Roscioni Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 11 Mar 2008 15:26:24 +0000 MIME-Version: 1.0 Sent to CCL by: Otello Maria Roscioni [omr]=[soton.ac.uk] Hello! I need an advice on how to build a nanoparticle starting from a crystallographic structure. I know that the gdis program has this feature on the Buildings=>Surfaces menu, but there is no manual available. Has somebody already used this program to do a similar task? Thank you very much for the help Otello M. Roscioni From owner-chemistry@ccl.net Tue Mar 11 13:41:00 2008 From: "Vincent Vivien vincent#eyesopen.com" To: CCL Subject: CCL: Final program for OpenEye's EuroCUP in Strasbourg, April 16-18, 2008 Message-Id: <-36480-080311122148-18502-vS6wvg2lmmd8TdzBoFhOgw.@.server.ccl.net> X-Original-From: "Vincent Vivien" Date: Tue, 11 Mar 2008 12:21:43 -0400 Sent to CCL by: "Vincent Vivien" [vincent!^!eyesopen.com] Dear Colleague, The final program for EuroCUP II, OpenEye's European science meeting held this year on April 16-18 in Strasbourg, France, is now available at: http://www.eyesopen.com/about/events/cup-eurocup/eurocup2-program-details.html It is also appended below. The deadline for registration is March 31st, although the conference hotel may no longer have rooms available for registrations made after March 15th, 2008. http://www.eyesopen.com/forms/eurocup2_reg.html There is no registration fee, delegates only need to cover travelling and accommodation. Poster submissions are still welcome until March 28th. We hope you will be able to join us in Strasbourg next month! Best regards, Vincent Vivien Director of European Accounts OpenEye Scientific Software vincent^^eyesopen.com Wednesday, April 16, 2008 ------------------------- [Pre-meeting Toolkit Session from 9:00 to 12:00] 13:30 Registration Tea, coffee. 14:15 Welcoming remarks, Anthony Nicholls, OpenEye Session 1: Shape & Electrostatics --------- 14:30 EPIC: Accurate Molecular Polarizabilities Based on Continuum electrostatics, Chris Bayly, Merck & Co 15:00 Mathematics, Shape Space and Other Marriages Made in Heaven, Paul Hawkins, OpenEye 15:30 Taming the Hydroxyl Rotor, Roger Sayle, OpenEye 16:00 Afternoon Break 16:30 Tackling GPCRs: Identification of Novel Non-peptidic Bradykinin B1 Receptor Antagonists via a Combination of Ligand and Structure-based Techniques, Uwe Richter, Jerini AG 17:00 Shape, Color and Pharmacophores: the Impact of Alignment on Virtual Screening, Gerhard Wolber, Inte:Ligand 17:30 End of session 1 19:00 Cocktail dinner and poster session Thursday, April 17, 2008 ------------------------ Session 2: Lead Optimization & Structure-based Design --------- 9:00 On the Impact of Virtual Screening in Genuine Lead Generation Campaigns, Stefan Schmitt, AstraZeneca 9:30 Fingerprinting Protein Cavities and Protein-ligand Complexes, Didier Rognan, CNRS 10:00 The Effects of Structural Changes on Molecular Properties: Matched Molecular Pair Analysis as a Tool for Lead Optimisation, Andrew Leach, AstraZeneca 10:30 Morning Break 11:00 Comparative Evaluation of Protein- and Ligand-based Virtual Screening Protocols, Andreas Evers, Sanofi-Aventis 11:30 Dirt Squad! - Confessions of an AgroScientist, John Delaney, Syngenta 12:00 End of session 2 and lunch 13:30 OpenEye Product Review: Ligand-based Design, Paul Hawkins, OpenEye Session 3: Prospective Science --------- 14:30 SAMPL Reprise: Nostradamus, Bohr, Weathermen & Us, Geoff Skillman, OpenEye 15:00 A decade of blind tests of crystal structure prediction: organisation, outcomes and future, Graeme Day, University of Cambridge 15:30 Afternoon Break 16:00 Ligand-based Methods for Inhibitors of Abeta Aggregation: Starting Points for Novel Alzheimers Therapeutics, Kim Branson, Stanford University 16:30 A Shape-based Journey from a Second Messenger to a Nanomolar Drug: NAADP to Ned-14, Grant Churchill, University of Oxford 17:00 End of session 3 17:15 Castalian Allocution: -------------------- Living in Castalia - The Pitfalls in 'Rational' Design, Hugo Kubinyi, BASF and University of Heidelberg (retired) 18:30 Departure for Barr wine cellar visit and conference dinner Friday, April 18, 2008 ---------------------- Session 4: Physical Property Prediction --------- 9:00 A Survey of Halogens: Dummkopf, Where Have You Put the Lone Pairs?, Peter Kenny, AstraZeneca 9:30 Unveiling the Janus Face of Organic Fluorine, Holger Gohlke, J.W. Goethe-University 10:00 Halogens, Smalogens: the Electrostatics of Awkward Compounds, Anthony Nicholls, OpenEye 10:30 Morning Break 11:00 Prediction of Aqueous Solubility in the Early Drug Discovery Phase, Bernd Beck, Boehringer-Ingelheim 11:30 Tales of the Unexpected Similarity, Jurgen Bajorath, University of Bonn 12:00 End of session 4 Concluding remarks, Anthony Nicholls, OpenEye Lunch and departure From owner-chemistry@ccl.net Tue Mar 11 15:03:00 2008 From: "Dr David N Haney haney]=[edusoft-lc.com" To: CCL Subject: CCL: calculating and displaying surface residues Message-Id: <-36481-080311140941-28612-kHFpkl7C2Iv+RIxPaBmfiw[a]server.ccl.net> X-Original-From: Dr David N Haney Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8 Date: Tue, 11 Mar 2008 09:54:24 -0700 Mime-Version: 1.0 Sent to CCL by: Dr David N Haney [haney : edusoft-lc.com] Dear Kalpana Krishnaswami, Although HINT is not freeware, it is one of the best tools to display hydrophobic energy surfaces as well as hydrophobic-hydrophobic surface interactions. HINT scoring has been shown to provide a good correlation with binding energy. It is currently available as a TOOLKIT and the libraries can be used with external programs like PyMol. Please see www.edusoft-lc.com/hint ++ J. Med. Chem. 1991, 34, 758-767. J. Computer Aided Mol. Design 1991, 5, 545-552. J. Med. Chem. 2003, 46, 4487-4500. J. Med. Chem. 2004, 47, 4507-4516. J. Mol. Biol. 2006, 358, 289–309. On Fri, Mar 07, 2008 at 09:21:04AM +0530, Kalpana Krishnaswami kalpuk*_*gmail.com wrote: > Hi > We would like to calculate and display exposed hydrophobic surfaces on a > protein. We would also like to list the residues on the surface. Are there > freeware/ scripts/plugins to pymol/rasmol that would do this? > Thanks > -- > Kalpana Krishnaswami -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney(a)edusoft-lc.com # ################# ##################### From owner-chemistry@ccl.net Tue Mar 11 15:37:00 2008 From: "Jim Kress ccl_nospam*|*kressworks.com" To: CCL Subject: CCL: 3D data visualisation software Message-Id: <-36482-080311142646-17692-hTH83QZKny6aN0hGTtZCpw+*+server.ccl.net> X-Original-From: "Jim Kress" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000D_01C8837E.55CBB2B0" Date: Tue, 11 Mar 2008 13:46:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam^-^kressworks.com] This is a multi-part message in MIME format. ------=_NextPart_000_000D_01C8837E.55CBB2B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable gnuplot? =20 http://www.gnuplot.info/ =20 Jim _____ =20 > From: andras.borosy_+_givaudan.com [mailto:owner-chemistry[#]ccl.net]=20 Sent: Tuesday, March 11, 2008 10:16 AM To: Kress, Jim Subject: CCL: 3D data visualisation software Dear all,=20 I would need simple and cheap 3D data visualisation software (in ideal = case an add in for Excel) like XLSAT 3D Plot (http://www.modeladvisor.com/specific_use/others/statistic_forecast/xlsta= t_3 dplot/xlstat_3dplot.htm).=20 Might you suggest me anything?=20 Many thank,=20 Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf = - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com ------=_NextPart_000_000D_01C8837E.55CBB2B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
gnuplot?
 
http://www.gnuplot.info/
 
Jim

From: andras.borosy_+_givaudan.com = [mailto:owner-chemistry[#]ccl.net]
Sent: Tuesday, March 11, = 2008=20 10:16 AM
To: Kress, Jim
Subject: CCL: 3D = data=20 visualisation software


Dear all, =

I would need simple and cheap = 3D data=20  visualisation software (in ideal case an add in for Excel) like = XLSAT 3D=20 Plot=20 = (http://www.modeladvisor.com/specific_use/others/statistic_forecast/xlsta= t_3dplot/xlstat_3dplot.htm).=20

Might you suggest me=20 anything?

Many = thank,=20

Dr. Andr=E1s P=E9ter = Borosy
Scientific=20 Modelling Expert
Fragrance Research
Givaudan Schweiz AG  -=20  Ueberlandstrasse 138  -  CH-8600  - =  D=FCbendorf=20  -  Switzerland
T:+41-44-824 2164  - =  F:+41-44-8242926=20    - =  http://www.givaudan.com ------=_NextPart_000_000D_01C8837E.55CBB2B0-- From owner-chemistry@ccl.net Tue Mar 11 16:18:00 2008 From: "David Hose Anthrax_brothers ~~ hotmail.com" To: CCL Subject: CCL:G: G03-SCRF calculations with hexane Message-Id: <-36483-080311161618-23744-omq1S9lBvWE7CUbkuSiEKA=-=server.ccl.net> X-Original-From: "David Hose" Date: Tue, 11 Mar 2008 16:16:14 -0400 Sent to CCL by: "David Hose" [Anthrax_brothers|-|hotmail.com] Marcel, Thanks for the tip about calculating the optical dielectric constant from the refractive index. I'm sure that I'll be using that very frequently. Andy, Thanks for the parameters for DMF and the tip about the OFac and RMin parameters when PCM calculation run amuck. Many thanks. Regards, Dave. Hi David, Jose, I had a similar problem with ADF, where the optical dielectric constant (EPSINF) was not directly given in the CRC handbook. However, then I asked around, and I got this helpful answer: > The optical dielectric constant is directly related to the > refractive index, eps_op = n^2. > The refractive index should be in the Handbook. On Mar 10, 2008, at 10:12 PM, David Hose anthrax_brothers_- _hotmail.com wrote: > > Sent to CCL by: "David Hose" [anthrax_brothers|*|hotmail.com] > Jose, > > Like you, I'm also trying to run PCM calculations in non-standard > solvents. Since my original post > I've been digging through the literature trying to find answers for > DMF and NMP. > > The Gaussian manual states that if you don't state values explicit > values for EPS, RSOLV, DENSITY > and EPSINF, then they default to the values for water (http:// > www.gaussian.com/g_ur/k_scrf.htm). > So just specifying the dielectric constant isn't enough. You could > just go with the values for > heptane (I doubt that it will make much of a difference). > > In the course of chasing down values for the solvent radii, I came > across an interesting paper by E.S. Boes et al., Chemical Physics, > 2006, 331, 142158 > (dx.doi.org/10.1016/j.chemphys.2006.08.028) They were looking at > the parameterisation of IEF- > PCM calculations of mono-anions in acetonitrile and DMF. The paper > cites Abraham and Liszi (J. > Chem. Soc. Faraday Trans. 1978, 74, 1604.) for the molecular radii > of the solvents which in turn > states that the radii of the solvents are calculated from the > Stearn - Eyring equation (A. E. Stearn > and H. Eyring. J. Chem. Phys., 1937, 5, 113). > > r=(V/8*Na)^(1/3) > > where r is the solvent radius (Angstroms), V is solvent molar > volume (m3 / mol), and Na is > Avogadro's constant. > > The EPSINV values are causing me a headache. Whilst the CRC Rubber > Handbook of Chemistry and > Physics has loads of information about the dielectric constant of > water at different temperatures, > pressures and frequencies, I can't find values for DMF and NMP. In > your case, I would either use the > value quoted for heptane (the output contains the values used in > the PCM calculation) or use the > default value for water which from memory is about 1 - 2 > (personally I'd use the value for heptane > in the absence of any better data). > > Hope that helps. > > Regards, > > Dave. > > > Sent to CCL by: "Jose P. Ceron" [jpceron(_)um.es] > Dear all, > I need to include solvent effects in TDDFT calculations to compare > my results with experimental > data. The problem is that the UV-Vis spectra are made in hexane and > this solvent is not define in > Gaussian. > I know EPS, RSOLV, DENSITY and EPSINF keyword can be used with PCM > model, > but is it enough to specify EPS(hexane)=2.0? > Any suggestion will be welcome!! > Thanks in advanced, > Jose > > ----------------------- > Jose P. Ceron > University of Murcia > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > =================================== dr. Marcel Swart ICREA researcher at Institut de Qumica Computacional Universitat de Girona Parc Cientfic i Tecnolgic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart**icrea.es marcel.swart**udg.edu web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.edu/~marcel =================================== From owner-chemistry@ccl.net Tue Mar 11 16:53:00 2008 From: "Alcides Simao alsimao(a)gmail.com" To: CCL Subject: CCL: 3D data visualisation software Message-Id: <-36484-080311162218-28147-sp8qHizWoyj0ae9XX6Nb4g^-^server.ccl.net> X-Original-From: "Alcides Simao" Content-Type: multipart/alternative; boundary="----=_Part_2600_24257779.1205266925101" Date: Tue, 11 Mar 2008 20:22:03 +0000 MIME-Version: 1.0 Sent to CCL by: "Alcides Simao" [alsimao=gmail.com] ------=_Part_2600_24257779.1205266925101 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline OpenOffice? Gnuplot? KOffice? GOffice? SciGraphica? Google worksheets? ------=_Part_2600_24257779.1205266925101 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline OpenOffice?
Gnuplot?
KOffice?
GOffice?
SciGraphica?
Google worksheets? ------=_Part_2600_24257779.1205266925101-- From owner-chemistry@ccl.net Tue Mar 11 17:28:00 2008 From: "Negi, Surendra S. ssnegi _ utmb.edu" To: CCL Subject: CCL: calculating and displaying surface residues Message-Id: <-36485-080311164854-14500-g/hHM0zXYbU0/cDjQSbwcA###server.ccl.net> X-Original-From: "Negi, Surendra S." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 11 Mar 2008 14:21:56 -0500 MIME-Version: 1.0 Sent to CCL by: "Negi, Surendra S." [ssnegi#,#utmb.edu] Use the Getarea website at http://pauli.utmb.edu/cgi-bin/get_a_form.tcl =20 good lcuk sn ________________________________ > From: Dr David N Haney haney]=3D[edusoft-lc.com = [mailto:owner-chemistry]-[ccl.net] Sent: Tue 3/11/2008 11:54 AM To: Negi, Surendra S. Subject: CCL: calculating and displaying surface residues Sent to CCL by: Dr David N Haney [haney : edusoft-lc.com] Dear Kalpana Krishnaswami, Although HINT is not freeware, it is one of the best tools to display hydrophobic energy surfaces as well as hydrophobic-hydrophobic surface = interactions. HINT scoring has been shown to provide a good correlation with binding = energy. It is currently available as a TOOLKIT and the libraries can be used = with external programs like PyMol. Please see www.edusoft-lc.com/hint ++ J. Med. Chem. 1991, 34, 758-767. J. Computer Aided Mol. Design 1991, 5, 545-552. J. Med. Chem. 2003, 46, 4487-4500. J. Med. Chem. 2004, 47, 4507-4516. J. Mol. Biol. 2006, 358, 289-309. On Fri, Mar 07, 2008 at 09:21:04AM +0530, Kalpana Krishnaswami = kalpuk*_*gmail.com wrote: > Hi > We would like to calculate and display exposed hydrophobic surfaces on = a > protein. We would also like to list the residues on the surface. Are = there > freeware/ scripts/plugins to pymol/rasmol that would do this? > Thanks > -- > Kalpana Krishnaswami -- ######### David N. Haney, Ph.D. ######### # EduSoft, LC Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney*_*edusoft-lc.com # ################# ##################### -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml= =20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt