From owner-chemistry@ccl.net Wed Nov 9 08:27:00 2005 From: "Kim Branson kim.branson\a/gmail.com" To: CCL Subject: CCL: Active site volume and surface exposure Message-Id: <-29908-051109012456-23627-wBzRzJXyANFlptQ3dmwg1g..server.ccl.net> X-Original-From: Kim Branson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Wed, 9 Nov 2005 16:27:51 +1100 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Kim Branson [kim.branson(~)gmail.com] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi all, I'm currently looking for a method that can determine the volume of an active site and its surface exposure. I'm conducting a validation study on protein-protein interaction inhibitors and i would like to quantify the oft heard expression "protein-protein interfaces are often flat featureless surfaces". I'd like to compare the binding sites to that of other systems, and hopefully examine the relationship between scoring function performance and active site volume/surface exposure. I have a crude metric using the ratio of the volume of the active site to the total solvent accessible surface of my defined binding region. I feel there might be a better way to do this. cheers Kim Dr Kim Branson Peter Doherty Fellow Protein Structure and Function St Vincents Institute for Medical Research 41 Victoria Parade, Fitzroy Victoria 3065, Australia. Phone: +613 9288 2480 Fax: +613 94162 676 Ph +613 9662 7136 kbranson(0)svi.edu.au kim.branson(0)gmail.com www.svi.edu.au "Reminds me of the time I went to Africa, someone forgot the corkscrew and we had to live on food and water for days." W.C. Fields -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.4 (Darwin) iD8DBQFDcYjX3QNu8KNs0LgRAsVtAJ0dMYOO7mDl3l2jeph79XC2iQprOQCfdbFg 5U16yVvtmUQlnldznHKeSnY= =AcpJ -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Wed Nov 9 09:48:00 2005 From: "Telkuni Tsuru telkuni .. venus.dti.ne.jp" To: CCL Subject: CCL:G: Multi-step ONIOM Message-Id: <-29909-051109092652-11785-KPPi6HPLg9IjMnTD0WXSQQ/./server.ccl.net> X-Original-From: "Telkuni Tsuru" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Wed, 9 Nov 2005 23:26:51 +0900 MIME-Version: 1.0 Sent to CCL by: "Telkuni Tsuru" [telkuni]-[venus.dti.ne.jp] Hello, CCLers. I like to ask the description of multi-step ONIOM job on Gaussian98W. For example, the following input is correct? ======= input ======== %Chk=NaCl #T ONIOM(HF/6-31G(d):HF/3-21G(d)) SP NaCl SinglePoint-1 Na(High) Cl(Low) 0,1 0,1 Na 2.000000 0.000000 0.000000 H Cl 0.000000 0.000000 0.000000 L --Link1-- %Chk=NaCl #T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read NaCl SinglePoint-2 Na(High) Cl(Low) 0,1 0,1 Na H Cl L ======= end of input ======= If you don't mind, please point out the wrong part and teach me correct description. Any responses I'll appreciate. I will summarize them and upload to this ML. Sincerely yours, ---------------------------------------------------- Telkuni Tsuru telkuni[-]venus.dti.ne.jp Bunshi Gijyutu [this "venus" means the planet "venus".] From owner-chemistry@ccl.net Wed Nov 9 11:04:01 2005 From: "errol lewars elewars-x-trentu.ca" To: CCL Subject: CCL:G: transition state searches with CASSCF ??? Message-Id: <-29910-051109102832-10194-Wk+b5qgVNseNQqT8BPfVZQ{}server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Wed, 09 Nov 2005 10:26:17 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars-,-trentu.ca] 2005 Nov 9 Hello, Yes, it is possible to find a TS at the CASSCF level with G03 (I used revision B.05); see J Phys Chem 2005, 109(43), 9827-9830. Start with a HF or MP2 structure, say, for the input geometry. Use corresponding MOs for the active space in comparing reactant, TS, and product. However your reaction, in which closed-shell molecules are transformed into radicals may give special problems in calculating the activation energy. EL ==== Theo de Bruin theodorus.de-bruin!^!ifp.fr wrote: >Sent to CCL by: "Theo de Bruin" [theodorus.de-bruin%a%ifp.fr] >Hello > >I wish to know whether it is possible to perform transition state searches at the CASSCF level of theory using Gaussian 03 rev C02. I asked the same question to the helpdesk of Gaussian but I gave up, after waiting more than 5 weeks. >I would like to study a bi-molecular reaction in which two (neutral) molecules are transformed into two radicals (reversed dismutation reaction). >Neither B3LYP nor X3LYP are capable to locate the TS, while unrestricted MP2 gives the correct TS but unusual high barrier (delta H activation) and delta H are obtained. > >Thanks for sharing your thoughts how to handle this problem. > >Kind regards, > >Theo de Bruin >theodorus.de-bruin . ifp.fr> > > > > From owner-chemistry@ccl.net Wed Nov 9 12:37:00 2005 From: "Elaine Meng meng|,|cgl.ucsf.edu" To: CCL Subject: CCL: Active site volume and surface exposure Message-Id: <-29911-051109123443-28595-1lXP93zWATjWcqWbiIZ5WA(!)server.ccl.net> X-Original-From: Elaine Meng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 9 Nov 2005 08:57:12 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Elaine Meng [meng ~ cgl.ucsf.edu] Hi Kim, The following papers used an RMS distance of interface atoms to a least-squares plane (there are many more papers, but these will get you started): Jones and Thornton. Prediction of protein-protein interaction sites using patch analysis. J Mol Biol. 1997 Sep 12;272(1):133-43. Chakrabarti and Janin. Dissecting protein-protein recognition sites. Proteins. 2002 May 15;47(3):334-43. Another measure I've seen is length to width to depth: Preissner, Goede, and Frommel. Dictionary of interfaces in proteins (DIP). Data bank of complementary molecular surface patches. J Mol Biol. 1998 Jul 17;280(3):535-50. Hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng{=}cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html > Sent to CCL by: Kim Branson [kim.branson(~)gmail.com] > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > Hi all, > > I'm currently looking for a method that can determine the volume of an > active site and its surface exposure. I'm conducting a validation > study > on protein-protein interaction inhibitors and i would like to quantify > the oft heard expression "protein-protein interfaces are often flat > featureless surfaces". I'd like to compare the binding sites to > that of > other systems, and hopefully examine the relationship between scoring > function performance and active site volume/surface exposure. > > I have a crude metric using the ratio of the volume of the active site > to the total solvent accessible surface of my defined binding > region. I > feel there might be a better way to do this. > > cheers > > Kim From owner-chemistry@ccl.net Wed Nov 9 13:11:00 2005 From: "Ferenc Csizmadia fcsiz^^^chemaxon.com" To: CCL Subject: CCL: InChI in Marvin, JChem, .... Message-Id: <-29912-051109125846-17775-symDzLKxK28Vc1o5rFyrgA * server.ccl.net> X-Original-From: Ferenc Csizmadia Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Wed, 09 Nov 2005 18:58:27 +0100 MIME-Version: 1.0 Sent to CCL by: Ferenc Csizmadia [fcsiz^chemaxon.com] Hi, (Sorry for cross-posting) InChI import and export have been added into ChemAxon tools (www.chemaxon.com/products.html) At the moment Linux, Windows and Mac platforms are supported, but we plan to add Sun and possibly HP Unix soon. InChI export can be tried most easily using the MarvinSketch applet, for example at http://www.chemaxon.com/marvin/doc/dev/example-sketch1.1.html. Draw a molecule and select Edit >> Source >> Format >> IUPAC InChI. If someone would like to have Marvin on his local machine, I suggest to download the Marvin Beans package from http://www.chemaxon.com/marvin/. (It is free for typical usages: http://www.chemaxon.com/prices.html) Regards, Ferenc From owner-chemistry@ccl.net Wed Nov 9 15:35:00 2005 From: "cristina menziani menziani-$-unimo.it" To: CCL Subject: CCL: call for applications:school of graduate studies Message-Id: <-29913-051109125008-5424-EB+uiOpNuFoxdqAKjHQr8g|a|server.ccl.net> X-Original-From: "cristina menziani" Sent to CCL by: "cristina menziani" [menziani{=}unimo.it] Universit degli Studi di Modena e Reggio Emilia School of graduate studies Multiscale Modelling, Computational Simulations and Characterization in Material and Life Sciences http://multiscale-school.unimore.it The School is aimed at providing students with a sound working knowledge of modern mathematical, computational and statistical modelling methods and algorithms as well as innovative experimental techniques for the characterization of complex systems at a multiscale level. The students will learn to apply this knowledge both in the field of material and life sciences working in multi-disciplinary well-integrated teams that emphasize the benefit of coordinated, iterative interactions between specialists in modelling/simulation and experimentalists. Topics in material and life sciences. Combinatorial and Numerical Algorithms, Computer Graphics, Chemo- and Bio-informatics, Experimental characterization of structures and properties, Human Computer Interface, Mathematical and computational Modelling, Neuroimaging, Statistical Modelling and Chemometrics. Doctoral Program This is a 3 years full-time course that includes introductory, basic and elective courses, seminars, tutorials, computer and experimental laboratory sessions and project work to produce a final dissertation on original themes of high standard in the international scientific framework. Stages in qualified research institutes in Italy and abroad are part of the student preparation as well. Possible positions achieved by graduated doctors. Students following this multi-disciplinary training will acquire the mathematical skills, chemical, engineering and biological insight, computational and experimental know-how necessary for tackling real-world problems. They will therefore be highly adaptable, with great employment prospects. Entry requirements. A second class honours degree or equivalent in a science, biotechnology, medicinal chemistry, medical or engineering subject. Admission is granted on a competitive basis. A Commission examines the CVs of the candidates and evaluates, in an interview (in Italian or English), their abilities to carry out research. Please refer to the Announcement published in the web site http://multiscale-school.unimore.it Scholarships The School awards 6 scholarships on a merit basis, two of which are reserved for candidates from universities other than the funding institution. Each scholarship is for about Euro 10.500 per year plus School tuition fees. The study grant is increased by 50% per month (for a maximum of 18 months) for time spent by the student at institutions abroad. For students who do not hold a scholarship, the tuition and registration fees amount to about Euro 1000 per year, depending on the income. Deadlines for application The notice of the competitive examination for the Doctoral Programs is issued Between October and November together with the number of places and scholarships available. The application for admission (www.unimore.it) must be submitted within 30 days of the published notice. Candidates are evaluated in December - January. The Courses begin on January-February1st. More info? scmamat*_*unimore.it Prof. Maria Cristina Menziani University of Modena and Reggio E. Department of Chemistry Via Campi 183 41100 Modena -Italy Tel: +39-059-2055091 Fax: +39-059-373543 E-mail: menziani*_*unimo.it From owner-chemistry@ccl.net Wed Nov 9 16:10:01 2005 From: "Steven Kirk steven.kirk.*o*.htu.se" To: CCL Subject: CCL: Ab initio simulations of ice-X Message-Id: <-29914-051109125718-17541-gb9EHjL0WCtMD5NZ66Sw1w*o*server.ccl.net> X-Original-From: "Steven Kirk" Sent to CCL by: "Steven Kirk" [steven.kirk#,#htu.se] Hello, I would like to ask if anyone on this list is aware of any ab initio electron structure calculations of the high-pressure ice phase ice-X. This is interesting as it has a Cu_{2}O -type structure, and the hydrogen bonds are centrosymmetric (i.e. the H atom is equidistant from both what would be conventionally regarded as the 'donor' and 'acceptor' O atoms). I have searched the Phys. Rev. and Nature indices, with no success thus far. I would be grateful for any pointers to literature or web pages of active researchers in this area. Many thanks in advance, Steve Kirk From owner-chemistry@ccl.net Wed Nov 9 18:47:00 2005 From: "Kim Baldridge kimb%%sdsc.edu" To: CCL Subject: CCL: Active site volume and surface exposure Message-Id: <-29915-051109154149-13428-bpIXV2T4DnZqxEt+U50tGw-.-server.ccl.net> X-Original-From: Kim Baldridge Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Wed, 9 Nov 2005 12:01:05 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Kim Baldridge [kimb|sdsc.edu] I think you meant another Kim, if I recall seeing the actual question from this person. Unfortunately, I can no look up her name since I am at another computer at home. -- ******************************************************* Kim Baldridge Prof. of Theoretical Chemistry, UniZH Director, Computational Applications, UniZH Distinguished Scientist, SDSC Adjunct Prof. Chemistry, UCSD mail: kimb{}sdsc.edu and kimb{}oci.unizh.ch http://www.oci.unizh.ch/group.pages/baldridge/site/ ******************************************************* On Wed, 9 Nov 2005, Elaine Meng meng|,|cgl.ucsf.edu wrote: > Sent to CCL by: Elaine Meng [meng ~ cgl.ucsf.edu] > Hi Kim, > The following papers used an RMS distance of interface atoms to > a least-squares plane (there are many more papers, but these will > get you started): > > Jones and Thornton. > Prediction of protein-protein interaction sites using patch analysis. > J Mol Biol. 1997 Sep 12;272(1):133-43. > > Chakrabarti and Janin. > Dissecting protein-protein recognition sites. > Proteins. 2002 May 15;47(3):334-43. > > Another measure I've seen is length to width to depth: > > Preissner, Goede, and Frommel. > Dictionary of interfaces in proteins (DIP). > Data bank of complementary molecular surface patches. > J Mol Biol. 1998 Jul 17;280(3):535-50. > > Hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. meng-.-cgl.ucsf.edu > UCSF Computer Graphics Lab and Babbitt Lab > Department of Pharmaceutical Chemistry > University of California, San Francisco > http://www.cgl.ucsf.edu/home/meng/index.html > >> Sent to CCL by: Kim Branson [kim.branson(~)gmail.com] >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> >> Hi all, >> >> I'm currently looking for a method that can determine the volume of an >> active site and its surface exposure. I'm conducting a validation >> study >> on protein-protein interaction inhibitors and i would like to quantify >> the oft heard expression "protein-protein interfaces are often flat >> featureless surfaces". I'd like to compare the binding sites to >> that of >> other systems, and hopefully examine the relationship between scoring >> function performance and active site volume/surface exposure. >> >> I have a crude metric using the ratio of the volume of the active site >> to the total solvent accessible surface of my defined binding >> region. I >> feel there might be a better way to do this. >> >> cheers >> >> Kim> > > From owner-chemistry@ccl.net Wed Nov 9 21:47:00 2005 From: "Loan H huynhkl2000 : yahoo.ca" To: CCL Subject: CCL: Drug-polymer interaction, diffusion of drug into polymer Message-Id: <-29916-051109214350-2812-k9O1BPVCf1+lObylc3KCPg*_*server.ccl.net> X-Original-From: "Loan H" Sent to CCL by: "Loan H" [huynhkl2000]*[yahoo.ca] Dear all, I am studying the simulation of drug-polymer interaction. I would appreciate very much if you could give me some suggestion of any drug-polymer interaction/diffusion simulation papers. So far, I was able to find 5 papers only about drug-polymer interaction/diffusion as listed below. Thank you very in advance. [1] Lam, Y.-M. et al. Mesoscale Simulation and cryo-TEM of Nanoscale Drug Delivery Systems. Molecular Simulation (2004) 30 (4), 239247 [2] Poupaerta, J.H. and Couvreur, P. A computationally derived structural model of doxorubicin interacting with oligomeric polyalkylcyanoacrylate in nanoparticles. Journal of Controlled Release (2003) 92, 19-26 [3] Li, J. et al. Prediction of drug solubility in an acrylate adhesive based on the drug-polymer interaction parameter and drug solubility in acetonitrile. Journal of Controlled Release (2002) 83, 211-221 [4] Li, T. et al. Computer simulation of molecular diffusion in amorphous polymers. J.Control.Release (1997) 48, 57. From owner-chemistry@ccl.net Wed Nov 9 22:21:01 2005 From: "Wei David Deng weidavid.deng*yale.edu" To: CCL Subject: CCL:G: Multi-step ONIOM Message-Id: <-29917-051106230120-61-i40jeT/OX3HJDJdG3YscMw{=}server.ccl.net> X-Original-From: Wei David Deng Date: Wed, 09 Nov 2005 12:07:11 -0500 Sent to CCL by: Wei David Deng [weidavid.deng===yale.edu] There are at least two parts are wrong. On the first step, you didn't specify the link atom and where the hydrogen should be put in the model system. You need to add "H" at the end of the chloride input. On the second step, you already said "geom=check", then you shouldn't enter the H and L levels again. It will automatic extract from the checkpoint file. I am attaching my input below. I hope this works in your system, since I am using a later version of Gaussian. Sincerely David Deng ================================================= %Chk=NaCl #T oniom(hf/6-31g(d):hf/3-21g*) sp Title Card Required 0 1 Na Cl 1 2.000 L H --Link1-- %Chk=NaCl #T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read NaCl SinglePoint-2 Na(High) Cl(Low) 0 1 ===================================== Wei David Deng wrote: > > Sent to CCL by: "Telkuni Tsuru" [telkuni]-[venus.dti.ne.jp] > Hello, CCLers. > > I like to ask the description of multi-step ONIOM job on Gaussian98W. > For example, the following input is correct? > > ======= input ======== > %Chk=NaCl > > #T ONIOM(HF/6-31G(d):HF/3-21G(d)) SP > > NaCl SinglePoint-1 Na(High) Cl(Low) > > 0,1 0,1 > Na 2.000000 0.000000 0.000000 H > Cl 0.000000 0.000000 0.000000 L > > --Link1-- > %Chk=NaCl > > #T ONIOM(HF/6-311+G(d,p):HF/6-31G(d)) SP Geom=Check Guess=Read > > NaCl SinglePoint-2 Na(High) Cl(Low) > > 0,1 0,1 > Na H > Cl L > > ======= end of input ======= > > If you don't mind, please point out the wrong part and teach me correct > description. > Any responses I'll appreciate. I will summarize them and upload to this ML. > > > Sincerely yours, > ---------------------------------------------------- > Telkuni Tsuru telkuni:venus.dti.ne.jp > Bunshi Gijyutu > [this "venus" means the planet "venus".]> > > > > -- Wei Deng (David), Ph.D. Post-doctoral Researcher Department of Chemistry, Yale University 225 Prospect St., P.O. Box 208107 New Haven, CT 06520-8107 Tel: (203) 284-2501 Email: weidavid.deng(0)yale.edu From owner-chemistry@ccl.net Wed Nov 9 22:57:00 2005 From: "Sue L chsue2004-.-yahoo.com" To: CCL Subject: CCL:G: Question for solvent field calcauation Message-Id: <-29918-051109221057-17459-/7FbA/XPK+YXQN80/Q18LA**server.ccl.net> X-Original-From: "Sue L" Sent to CCL by: "Sue L" [chsue2004:+:yahoo.com] Hi, I run a cpcm (CH3CN) calculation in Gaussian 03 for a molecule with the D2d symmetry. However, the calculation terminated abnormally with the following error message. Using symmetry in molecular cavity generation. AdVTs1: ISph= 839 is engulfed by JSph= 847 but Ae( 839) is not yet zero! Error termination via Lnk1e in /fs/home/app/g03c02/g03/l301.exe I found that there is a NOSYMMCAV keyword from Gaussian manual, which allows the calculation not imposing the molecular symmetry to the cavity. SymmCav is the default. I run a cpcm calulation by using NOSYMMCAV keyword. The calculation normally terminated. However, I found the following warning messages in the output. Warning! D(1802,1954)=0.40657557D+02 is big! D(1802,1802)=0.27113016D+02 D(1954,1954)=0.46253648D+02 Warning! D(1812,1963)=0.40657557D+02 is big! D(1812,1812)=0.27113016D+02 D(1963,1963)=0.46253648D+02 Warning! D(1954,1802)=0.40657557D+02 is big! D(1954,1954)=0.46253648D+02 D(1802,1802)=0.27113016D+02 Warning! D(1963,1812)=0.40657557D+02 is big! D(1963,1963)=0.46253648D+02 D(1812,1812)=0.27113016D+02 Does anyone know whether the NOSYMMCAV is required in the solvent field calculation for the molecule with symmetry? Also, what are these warning messages corresponding to? Best regards, Sue