From owner-chemistry@ccl.net Tue Nov 25 01:45:00 2008 From: "Leyla Ramin lram5228%%usyd.edu.au" To: CCL Subject: CCL: Ewald Sum Message-Id: <-38167-081124221431-2594-uF/iNo5GcWLCce+QB+dQNQ[-]server.ccl.net> X-Original-From: "Leyla Ramin" Date: Mon, 24 Nov 2008 22:14:27 -0500 Sent to CCL by: "Leyla Ramin" [lram5228[A]usyd.edu.au] I am PhD student in Sydney university and I am working in molecular dynamic simulation, The codes in fortran language in your website in part:sources, allen-tildesley-book "http://www.ccl.net/cca/software/SOURCES/FORTRAN/allen-tildesley-book/index.shtml>" is so useful for me. In the "FICHE F.22. ROUTINES TO PERFORM THE EWALD SUM" the routine is so complicated to understand the method. I am wondering if I can get more information about this code. Please kindly advise me and thanks for your consideration. Best Regards Leyla Ramin From owner-chemistry@ccl.net Tue Nov 25 03:57:00 2008 From: "Lukasz Cwiklik cwiklik(!)gmail.com" To: CCL Subject: CCL: Ewald Sum Message-Id: <-38168-081125035033-31068-BBkg+rJ+WRfzk1XlkoZxTw-x-server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 25 Nov 2008 10:50:20 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik%a%gmail.com] Dear Leyla, As the code is from Allen&Tildesley book look into the book for the details. Fortunately, the pages where the Ewald summation and the code are described are available for free at Google Books. Here is the link (Ch. 5.5.2, p. 156): http://tinyurl.com/626652 Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com On Tue, Nov 25, 2008 at 5:14 AM, Leyla Ramin lram5228%%usyd.edu.au wrote: > > Sent to CCL by: "Leyla Ramin" [lram5228[A]usyd.edu.au] > I am PhD student in Sydney university and I am working in molecular dynamic simulation, The codes in fortran language in your website in part:sources, allen-tildesley-book "http://www.ccl.net/cca/software/SOURCES/FORTRAN/allen-tildesley-book/index.shtml>" > is so useful for me. > In the "FICHE F.22. ROUTINES TO PERFORM THE EWALD SUM" the routine is > so complicated to understand the method. I am wondering if I can get more information about this code. > Please kindly advise me and thanks for your consideration. > > Best Regards > Leyla Ramin> > > -- Lukasz Cwiklik http://cwiklik.wordpress.com From owner-chemistry@ccl.net Tue Nov 25 04:35:01 2008 From: "Lukasz Cwiklik cwiklik-#-gmail.com" To: CCL Subject: CCL:G: van der Waals parameters for Ti Message-Id: <-38169-081125041507-8385-qZ4XzJUqunxVEVxADJqfxA..server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 25 Nov 2008 11:14:53 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [cwiklik[]gmail.com] Dear Saurabh, I do not know any tutorial, however, I will try to describe the general procedure. The way to estimate vdW parameters with ab initio (eg. Gaussian) is to scan a potential energy surface for interactions between your atom (rutile) and the atoms/molecules which rutile will interact with in your simulation. In the simples case, if you have just rutile-rutile interactions, make a scan of energy in Gaussian for changing the rutile-rutile distance. Then assume the parameters for rutile (for starters, take radius and well depth for a similar atom) and make the same scan in your MD code. Then the hard part starts - you need to fit (just by hand or write a code) the radius and well depth to have an agreement between ab initio and the empirical energy vs. distance curve (in a range of method's error which sometimes can be as high as 2 kcal/mol). One should remember about the basis set superposition error, however, there is no ideal method to get rid of bsse in this case. Best, Lukasz -- Lukasz Cwiklik http://cwiklik.wordpress.com On Mon, Nov 24, 2008 at 4:02 PM, Saurabh Agrawal Saurabh.Agrawal^^ucdconnect.ie wrote: > > Sent to CCL by: "Saurabh Agrawal" [Saurabh.Agrawal/./ucdconnect.ie] > Dear CCl users, > > I am trying to get non bonded parameters (van der Waals' radius and well depth) for Ti atom (rutile). I appreciate if some one could provide these parameters to me or let me know the way (tutorial) to calculate these parameters using Gaussian. > > Thanking you in advance. > > Best, > > Saurabh Agrawal, > PhD student, > University College Dublin, > Ireland> > > From owner-chemistry@ccl.net Tue Nov 25 05:38:00 2008 From: "Alexander Kos software[a]akosgmbh.eu" To: CCL Subject: CCL: PDB: structures with approved drugs Message-Id: <-38170-081125051806-10514-8jiVtsqljuZtRc5Gs2Jbrw++server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Date: Tue, 25 Nov 2008 10:46:04 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software()akosgmbh.eu] Dear Mr. Schmidt There is probably no databases with the details that you desire. = However, we sell for academia a package of databases that contains = Comprehensive Medicinal Chemistry. This includes most of the active = ingredients of drugs on the market. The Drug Data Report database = contains most compounds that are under investigation. In both databases = you have 2D structures, biological activities and additional data. The = in-house version contain also the Corina generated 3D structures. With = the Isentris front end you can use a conformationally flexible 3D = search, that allows to search over all conformations, even though only = one conformation is stored in the database. With best regards, Alexander Kos AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067=20 Fax (to mail): +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software|a|akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, = General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. (www.symyx.com), DIMENSION = 5, Ltd. (www.miner3d.com), CompuDrug International (www.compudrug.com), = Molecular Networks GmbH (www.mol-net.de), and others. -----Original Message----- > From: owner-chemistry+software=3D=3Dakosgmbh.eu|a|ccl.net = [mailto:owner-chemistry+software=3D=3Dakosgmbh.eu|a|ccl.net] On Behalf Of = Peter Schmidtke pschmidtke*|*mmb.pcb.ub.es Sent: Montag, 24. November 2008 23:27 To: Kos, Alexander J. Subject: CCL: PDB: structures with approved drugs Sent to CCL by: Peter Schmidtke [pschmidtke%x%mmb.pcb.ub.es] Dear CCLers, I have certainly a standard question that might appear often. Anyway, I would like to know if there is a comprehensive list of approved and marketed drugs with a corresponding PDB structure with the drug actually inside? The Drugbank only provides information about the targets, but = not this detail. Thanks in advance. Best regards. --=20 Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Nov 25 06:16:02 2008 From: "Vincent Leroux vincent.leroux*o*loria.fr" To: CCL Subject: CCL: Ewald Sum Message-Id: <-38171-081125050537-3912-dZAAYqL1AYVv6agw14YamQ ~~ server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Nov 2008 10:24:14 +0100 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux,+,loria.fr] Hi Leyla, You really should not try to understand Ewald sum method straight from source code, even if in this case it is well documented. The Ewald sum is done in Fourier space so first make sure you master this mathematical concept. http://en.wikipedia.org/wiki/Fourier_transformation http://en.wikipedia.org/wiki/Ewald_summation Then if you want, try to see how the conversion to Fourier space is handled in the code, how the summation is done, how code is optimized so that terms that can be computed once and for all are grouped in the setup routine, etc. The routine here is particularly simple! Actual MD programs such as NAMD rely on the same principles but with a good number of additional optimizations, in particular the code is heavily parallelized. This is much more complex, hopefully you do not need to master the code in order to understand and perform MD... For theoretical basis of molecular mechanics I strongly recommend you read A.R.Leach's book, if not done already. http://www.booksites.net/leach2/molecular/molecular_modelling_2.html Good luck for your PhD ^^ VL Leyla Ramin lram5228%%usyd.edu.au a écrit : > Sent to CCL by: "Leyla Ramin" [lram5228[A]usyd.edu.au] > I am PhD student in Sydney university and I am working in molecular dynamic simulation, The codes in fortran language in your website in part:sources, allen-tildesley-book "http://www.ccl.net/cca/software/SOURCES/FORTRAN/allen-tildesley-book/index.shtml>" > is so useful for me. > In the "FICHE F.22. ROUTINES TO PERFORM THE EWALD SUM" the routine is > so complicated to understand the method. I am wondering if I can get more information about this code. > Please kindly advise me and thanks for your consideration. > > Best Regards > Leyla Ramin > > From owner-chemistry@ccl.net Tue Nov 25 06:48:01 2008 From: "Jean-Christophe Poully poully%a%galilee.univ-paris13.fr" To: CCL Subject: CCL: Iinduced Fit Docking with Prime and Glide Message-Id: <-38172-081125054206-21331-WqZzB7pbKs/mARKt/9zl/A]![server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Tue, 25 Nov 2008 11:41:44 +0100 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully..galilee.univ-paris13.fr] Dear CCLrs, I am a newbie using the Induced Fit Docking=20 softwares from Schr=F6dinger, Prime and Glide, and=20 I am trying to dock a small ligand to Beta=20 Amyloid. The protein preparation, Glide first=20 docking and determination of residues for=20 refinement steps succeeded but unfortunately the=20 Prime active site refinement failed and I found=20 in the log file that all the jobs died because=20 the "SEQ_FILE option" was not specified. I have=20 no idea of what happened, if somebody has a clue=20 it would be really great! Thank you very much by advance... Best regards, Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Tue Nov 25 07:23:01 2008 From: "zborowsk]*[chemia.uj.edu.pl" To: CCL Subject: CCL:G: Raman intensity Vs Static polarizability Message-Id: <-38173-081125055356-28603-djHQ9ISeOlAZ8QJvKJTNnQ~~server.ccl.net> X-Original-From: zborowsk++chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 25 Nov 2008 11:53:42 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: zborowsk|,|chemia.uj.edu.pl Hi Dear Mi Yang I want to warn you if you are Gaussian user. Gaussian does not calculate Raman Intensities Sent to CCL by: favaro [laurent.favaro|*|u-psud.fr] Raman intensity is related to the square of the derivative of polarizability with respect to the normal coordinates of the vibrationnal mode. Best regards, Dr Favaro Mi Yang miyang3790_+_gmail.com a écrit : Sent to CCL by: "Mi Yang" [miyang3790*gmail.com] Dear CCL users, I need some comments or refs about my problem. I am studying the interaction of a metal with a boron cluster. I found the large increase of static polarizability and hyperpolarizability upon interaction of metal atom to that boron cluster. I also calculated the Raman spectrum which also showed high increase of intensity in metal boron cluster. I read some indirect relationship b/m these two properties but now in spite of my best efforts I could not find the direct relationship between Static polarizability and Raman intensity. Anybody who knows any ref or comments about this relationship (Static polarizability/hyperpolarizability and Raman intensity) would be highly appreciated.? Miyang P.R.China> -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk*chemia.uj.edu.pl gg 3817259 skype kzys70 www.chemia.uj.edu.pl/~zborowsk From owner-chemistry@ccl.net Tue Nov 25 07:57:01 2008 From: "Karin Wichmann wichmann{=}cosmologic.de" To: CCL Subject: CCL: COSMOtherm / COSMO-RS Training Message-Id: <-38174-081125073208-5462-7jb4iJb3bU5U1Mj7msU9vw/./server.ccl.net> X-Original-From: Karin Wichmann Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Tue, 25 Nov 2008 12:52:02 +0100 MIME-Version: 1.0 Sent to CCL by: Karin Wichmann [wichmann{}cosmologic.de] COSMOlogic has a small number of seats available for a free COSMOtherm training on December 8. The training is a one-day course covering COSMO-RS theory for fluid thermodynamics and its applications in the areas of chemical engineering and life science. The course will take place at our location in Leverkusen (Germany). For further information please contact us at cosmotherm (AT) cosmologic.de -- ------------------------ Dr. Karin Wichmann COSMOlogic GmbH & Co. KG Burscheider Str. 515 D-51381 Leverkusen Germany Phone +49-2171-73168-3 Fax +49-2171-73168-9 ------------------------ From owner-chemistry@ccl.net Tue Nov 25 09:31:01 2008 From: "amine amine m-22#%#hotmail.fr" To: CCL Subject: CCL: carbon and hydrogen negative charges Message-Id: <-38175-081125092947-25790-jp64nWZS1c/ro17p/7t/JQ^server.ccl.net> X-Original-From: "amine amine" Date: Tue, 25 Nov 2008 09:29:43 -0500 Sent to CCL by: "amine amine" [m-22|a|hotmail.fr] Hello in a ESP calculation by Guassian, I got negative charges for hydrogen and carbon. could you tell me the cause?. Thanks From owner-chemistry@ccl.net Tue Nov 25 12:33:01 2008 From: "Nicola Giacche nicolag%chimfarm.unipg.it" To: CCL Subject: CCL: Iinduced Fit Docking with Prime and Glide Message-Id: <-38176-081125083920-8773-5D/tWg1vrepnJbkv8NqSgw()server.ccl.net> X-Original-From: "Nicola Giacche'" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 25 Nov 2008 14:02:20 +0100 MIME-Version: 1.0 Sent to CCL by: "Nicola Giacche'" [nicolag]*[chimfarm.unipg.it] directly you can ask to help(at)schrodinger.com to have the correct answer. bye Jean-Christophe Poully poully%a%galilee.univ-paris13.fr ha scritto: > > Sent to CCL by: Jean-Christophe Poully [poully..galilee.univ-paris13.fr] > > Dear CCLrs, > > I am a newbie using the Induced Fit Docking softwares from > Schrödinger, Prime and Glide, and I am trying to dock a small ligand > to Beta Amyloid. The protein preparation, Glide first docking and > determination of residues for refinement steps succeeded but > unfortunately the Prime active site refinement failed and I found in > the log file that all the jobs died because the "SEQ_FILE option" was > not specified. I have no idea of what happened, if somebody has a clue > it would be really great! Thank you very much by advance... > > Best regards, > > > > > Jean-Christophe Poully > > Doctorant dans l'équipe AMIBES > Laboratoire de Physique des Lasers > Institut Galilée > 99, avenue JB Clément > 93430 VILLETANEUSE > > Bureau B002 > 0149403853 > > > -=his is automatically added to each message by the mailing script =-http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Nicola Giacchè, PhD Student Bachelor Degree in Medicinal Chemistry and Technology of Drugs University of Perugia Department of Medicinal Chemistry and Technology of Drugs Via del Liceo, 1 - 06123 Perugia (Italy) Tel ++39 075 585 5169/5156 E-mail: nicolag---chimfarm.unipg.it From owner-chemistry@ccl.net Tue Nov 25 15:36:00 2008 From: "Hugo Merlos merlos.aritzmendi.(!).gmail.com" To: CCL Subject: CCL: AutoDock Cu parameters Message-Id: <-38177-081125130733-6922-rBOA9gHi1Cm6lbpm2wlSjQ(!)server.ccl.net> X-Original-From: "Hugo Merlos" Date: Tue, 25 Nov 2008 13:07:29 -0500 Sent to CCL by: "Hugo Merlos" [merlos.aritzmendi^^^gmail.com] Hi everybody! Someone can help me?... I need the parameters of copper for input in the data values (AD4_parameters.dat file)... Thanks in advance. From owner-chemistry@ccl.net Tue Nov 25 18:10:00 2008 From: "favaro laurent.favaro:_:u-psud.fr" To: CCL Subject: CCL:G: Raman intensity Vs Static polarizability Message-Id: <-38178-081125170705-16006-7pB8CCeJes4V+1jLUcwD0w||server.ccl.net> X-Original-From: favaro Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-2; format=flowed Date: Tue, 25 Nov 2008 23:06:54 +0100 MIME-Version: 1.0 Sent to CCL by: favaro [laurent.favaro[#]u-psud.fr] Do you mean that G03 does not calculate Raman Cross-section ? I believe you are wrong. Regards. LF zborowsk]*[chemia.uj.edu.pl a écrit : > Sent to CCL by: zborowsk|,|chemia.uj.edu.pl > Hi > Dear Mi Yang > I want to warn you if you are Gaussian user. > Gaussian does not calculate Raman Intensities > > > > Sent to CCL by: favaro [laurent.favaro|*|u-psud.fr] > Raman intensity is related to the square > of the derivative of polarizability with respect > to the normal coordinates of the vibrationnal mode. > Best regards, > Dr Favaro > Mi Yang miyang3790_+_gmail.com a écrit : > > Sent to CCL by: "Mi Yang" [miyang3790*gmail.com] > Dear CCL users, > I need some comments or refs about my problem. I am studying the > interaction of a metal with a boron cluster. I found the large increase > of static polarizability and hyperpolarizability upon interaction of > metal atom to that boron cluster. I also calculated the Raman spectrum > which also showed high increase of intensity in metal boron cluster. I > read some indirect relationship b/m these two properties but now in spite > of my best efforts I could not find the direct relationship between > Static polarizability and Raman intensity. Anybody who knows any ref or > comments about this relationship (Static > polarizability/hyperpolarizability and Raman intensity) would be highly > appreciated.? > Miyang > P.R.China> >