From owner-chemistry@ccl.net Tue Aug 9 02:26:00 2011 From: "Kamalakar Jadhav kjadhav!A!vlifesciences.com" To: CCL Subject: CCL: VLife advances with release of VLifeMDS 4.0 Message-Id: <-45227-110809022257-31984-Mq1Mdq8sq5MgWcUTJHqT/A,+,server.ccl.net> X-Original-From: "Kamalakar Jadhav" Date: Tue, 9 Aug 2011 02:22:53 -0400 Sent to CCL by: "Kamalakar Jadhav" [kjadhav*_*vlifesciences.com] Dear All, We are very pleased to announce that the VLifeMDS, one of the most advanced package in molecular modeling has now released VLifeMDS 4.0 Following are the key advancements with VLifeMDS: * Enhanced Graphics Improved channel and cavity surfaces Fast Connoly surface generation Intuitive Ramachandran plot * Advanced Homology Modeling Auto Homology modeling Support for new sequence database from RCSB Intuitive modification and model building Multi template Homology modeling * Advancement in GRIP Docking Ligand wise systematic output Improved performance with speed * LeadGrow Virtual library generation Applicability domain check GRIP docking based screening kNN-MFA based screening * Advanced LeadGrow Multi template combinatorial library generation * VLife QSARPlus Applicability domain check Contour visualization with PLS MFA Multiple response QSAR modeling * AutoQSAR workflow for multiple model building * SCOPE: Score based method for lead optimization * Structure based pharmacophore generation * GLib: Combinatorial library generation using GQSAR model * GQSAR model based activity optimization with GUI * Multicore enabled * Scripting Python Integration Script console Command line support on Linux CCL members can avail the VLifeMDS 4.0 free license coupon at http://blog.vlifesciences.com Best Regards, Kamalakar Jadhav VLife Sciences From owner-chemistry@ccl.net Tue Aug 9 06:25:01 2011 From: "Andreas Bender, PhD ab454/a\cam.ac.uk" To: CCL Subject: CCL: Final Reminder: MGMS Event "Connecting Structure to Function", Cambridge, 19-21 September 2011 Message-Id: <-45228-110809052740-9880-aNFWrOSxLbTqfvTpwaXihg:_:server.ccl.net> X-Original-From: "Andreas Bender, PhD" Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 09 Aug 2011 10:26:46 +0100 Mime-Version: 1.0 Sent to CCL by: "Andreas Bender, PhD" [ab454:cam.ac.uk] Dear CCL'lers, Dear Cambridge Cheminformatics Friends, For those of you interested to participate but who didn't register yet, we would like to cordially invite you to an MGMS meeting in Cambridge (UK) on the topic of "Connecting Structure to Function: From Calculation to Experiment and Back Again" [ http://www.mgms.org/JGV_meeting/index.html ], an event organized to recognize and honour Andy Vinter and his contributions to the fields of computer-aided drug design and, more generally, intermolecular interactions and their driving forces. The meeting will take place from 19-21 September 2011, at Downing College, Cambridge and we already have an impressive list of confirmed speakers which should make this event a very memorable one (see http://www.mgms.org/JGV_meeting/speakers.html for more information). For further details and registration (which will close shortly) please visit the conference website at the following address: http://www.mgms.org/JGV_meeting/index.html Best wishes and we are looking forward to welcoming you to Cambridge in September! Cheers, Andreas -- Andreas Bender, PhD Lecturer for Molecular Informatics Unilever Centre, Cambridge University http://www-ucc.ch.cam.ac.uk Personal: http://www.andreasbender.de From owner-chemistry@ccl.net Tue Aug 9 08:37:00 2011 From: "Jaroslaw Pawlak j.pawlak**fqs.pl" To: CCL Subject: CCL: Molecular dynamics in materials Message-Id: <-45229-110809025317-19242-iuDx584H1PjfQPE3ZDf2wA.@.server.ccl.net> X-Original-From: Jaroslaw Pawlak Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 09 Aug 2011 08:53:07 +0200 MIME-Version: 1.0 Sent to CCL by: Jaroslaw Pawlak [j.pawlak : fqs.pl] Hello, You may try to use SCIGRESS (www.fqs.pl/SCIGRESS). It includes about 60 potentials dedicated for materials mainly. Best wishes Jaroslaw Pawlak On 8/7/2011 11:51 AM, Olalla Nieto Faza faza]=[uvigo.es wrote: > > Sent to CCL by: Olalla Nieto Faza [faza{}uvigo.es] > I'm interested in performing some molecular dynamics simulations in > materials (both crystalline and amorphous phases) using interatomic > potentials (not ab-initio MD). > Do you know of any available code (either commercial or not) that could > be suitable for this, or do you use our own programs for this? > > > Regards, > > Olalla > From owner-chemistry@ccl.net Tue Aug 9 09:12:00 2011 From: "Dan Maftei dan.maftei=uaic.ro" To: CCL Subject: CCL:G: Molecular dynamics in materials Message-Id: <-45230-110809020947-32115-+/EbPwLwHMxpl7ZvwtHawg{:}server.ccl.net> X-Original-From: Dan Maftei Content-Type: multipart/mixed; boundary="------------050103030209020507050901" Date: Tue, 09 Aug 2011 09:09:32 +0300 MIME-Version: 1.0 Sent to CCL by: Dan Maftei [dan.maftei:+:uaic.ro] This is a multi-part message in MIME format. --------------050103030209020507050901 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear Olalla, Here is a list of codes I've used to model some crystalline metal oxides: 1. DL_POLY. Version 2 became now DL_POLY CLASSIC and is available open source trough CCPForge (http://ccpforge.cse.rl.ac.uk/gf/). Improved versions 3 and 4 are also available upon registration (http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/index.shtml). A quite nice GUI also exists, except it is written in Java and doesn't make use of the 3D capabilities of your graphic card. To visualize atomic trajectories recorded in a Molecular Dynamics simulation, as well as to compute radial distribution functions, atomic displacement and so on, a better choice is VMD (Visual Molecular Dynamics) and it's DL_POLY 2/3 plugin (included "out of the box"). 2. GULP (http://projects.ivec.org/gulp/). I'd recommend GULP for "static calculations", i.e. structural optimization, potential testing and fitting to measured properties, defect calculations, phase transitions and so. If interested in Molecular Dynamics in ionic materials you should consider DL_POLY, which performs better/faster. GDIS (http://gdis.sourceforge.net/) is a nice GUI designed to work with GULP, unfortunately it's (a bit?) outdated and poorly maintained. 3. MOLDY (http://www.ccp5.ac.uk/moldy/moldy.html). It looks similar to DL_POLY but supports only pair potentials, is written in C (could be slower?) and has a MPI implementation whose compilation should be straightforward on a gcc/mpich2 enabled Linux. You'll also find these codes are the most cited in papers reporting atomistic simulations of materials. Regards, Dan. Pe 07.08.2011 12:51, Olalla Nieto Faza faza]=[uvigo.es a scris: > > Sent to CCL by: Olalla Nieto Faza [faza{}uvigo.es] > I'm interested in performing some molecular dynamics simulations in > materials (both crystalline and amorphous phases) using interatomic > potentials (not ab-initio MD). > Do you know of any available code (either commercial or not) that could > be suitable for this, or do you use our own programs for this? > > > Regards, > > Olalla > -- Dan Maftei, Assistant Professor, Faculty of Chemistry/Department of Chemistry University Alexandru Ioan Cuza Iasi Bd. Carol 1, Nr. 11, 700506 Iasi, Romania Tel: +40 232 201307 E-mail(s): dan.maftei * chem.uaic.ro dan.maftei * uaic.ro --------------050103030209020507050901 Content-Type: application/pgp-keys; name="0xF59B8983.asc" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="0xF59B8983.asc" -----BEGIN PGP PUBLIC KEY BLOCK----- Version: GnuPG v2.0.14 (GNU/Linux) mQGiBEjrO0wRBACQkJChhDxP3N+/d5o1B/6TCA54b9w+qbhDnW7GK/wZDunsmEKY XVsAcWt+O32NHVekEyOBYetR8wctmyWogIjn9YZznk/PkQzZhqL6bD4MirXbyBvP MiII7iF1T+Ou7tiv7UbmpwRYX2Wb02ey51i0qdq9WQ1E+XATmifzXGGFIwCg3u/O +oyu37f+7hm92q1Ls20AxrsD/jN2Fh7yjl0erV4Sy/USe+CS+lKWZDAMkCFj5wTe +SqTPWtN0GKfiWeXjgUBCdRCktVfOEHjo0bcpnYpm7BY7hnGbD7+ceO2dSvCFRf2 NWmWpDgW6+zLKhuoMpVYwYtkGD0v9as14MQJyDyZewonP5mPwN/aMBA12iPOifQ4 Pgw9A/4mvsmoTLnSPkoauLoU+mRKbGFGBNUeLUFfzxLxcOei5BrRg3nKLW9p+sUZ tVdMPbpWSAf88HambwFR6TOwmwrX0pbRo5gucWga6txESPP8cw2FA9CTpSn+CrIO iqPRr+g48yoMYiWGT4t2PalrEgof+yyE+75It5Io7ihUzix2jbQkRGFuIE1hZnRl 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To this end, does anyone know of an available conversion utility (.mol <--> .mol2), or the location of some example structure files in both formats? I found an old babel version on CCL, however, it does not run correctly on my Windows7 platform. Thanks -Arthur From owner-chemistry@ccl.net Tue Aug 9 18:22:01 2011 From: "Giuseppe Mallia g.mallia^_^imperial.ac.uk" To: CCL Subject: CCL: MSSC2011 - London Edition - Final call Message-Id: <-45232-110809181425-723-/Uwc7qogDMMO1pFcXLoQEw|server.ccl.net> X-Original-From: "Giuseppe Mallia" Date: Tue, 9 Aug 2011 18:14:22 -0400 Sent to CCL by: "Giuseppe Mallia" [g.mallia]*[imperial.ac.uk] Final call: ~~~~~~~~~~~~~~~~~~~~~~~~~~ MSSC2011 - Ab initio Modelling in Solid State Chemistry London Edition (New Users): Discovering quantum-mechanical simulations with CRYSTAL http://www.cse.scitech.ac.uk/events/MSSC2011/ London (UK), September 19-23, 2011 Directors: N.M. Harrison - G. Mallia The week long school is designed for CRYSTAL users, PhD students, Post-Docs and researchers with interests in solid state chemistry, physics, materials science, surface science, catalysis, magnetism and nano-science. It will provide both an introduction to the capabilities of quantum mechanical simulation and to the practical use of CRYSTAL09 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-chemistry@ccl.net Tue Aug 9 20:14:01 2011 From: "Daniel Glossman-Mitnik dglossman ~ gmail.com" To: CCL Subject: CCL: old Sybyl *.mol file format Message-Id: <-45233-110809181012-19212-gA2g4uNoqkx/4DzF8I6arw^_^server.ccl.net> X-Original-From: Daniel Glossman-Mitnik Content-Type: multipart/alternative; boundary=000325557a620dcf8e04aa19a024 Date: Tue, 9 Aug 2011 15:55:42 -0600 MIME-Version: 1.0 Sent to CCL by: Daniel Glossman-Mitnik [dglossman ~~ gmail.com] --000325557a620dcf8e04aa19a024 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Arthur: Try OpenBabel http://openbabel.org Best regards, Daniel ***************************************************************************= ************************************ Dr. Daniel Glossman-Mitnik Centro de Investigaci=C3=B3n en Materiales Avanzados, SC Departamento de Simulaci=C3=B3n Computacional y Modelado Molecular Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih 31109, Mexico Phone: +52 614 4391151 Secretary/FAX: +52 614 4391130 Lab: +52 614 4394805 E-mail: daniel.glossman:+:cimav.edu.mx dglossman:+:gmail.com WWW: http://www.cimav.edu.mx/cv/daniel.glossman http://blogs.cimav.edu.mx/daniel.glossman ***************************************************************************= ************************************ 2011/8/9 Arthur Doweyko adoweyko%x%comcast.net > > Sent to CCL by: "Arthur Doweyko" [adoweyko|a|comcast.net] > I'm in the midst of rewriting some old code which made use of the old, no= w > defunct, Sybyl *.mol file format (not to be confused with the MDL *.mol > format). To this end, does anyone know of an available conversion utilit= y > (.mol <--> .mol2), or the location of some example structure files in bot= h > formats? > I found an old babel version on CCL, however, it does not run correctly o= n > my Windows7 platform. > Thanks > > -Arthur > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --000325557a620dcf8e04aa19a024 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear Arthur:

Try =C2=A0OpenBabel =C2=A0 http://openbabel.org

Best reg= ards,

Daniel

************= ***************************************************************************= ************************
Dr. Daniel Glossman-Mitnik
Centro de Investigaci=C3=B3n en Materiales Av= anzados, SC
Departamento de Simulaci=C3=B3n Computacional y Modelado Mol= ecular
Miguel de Cervantes 120 - Comp. Ind. Chihuahua - Chihuahua, Chih = 31109, Mexico
Phone: +52 614 4391151=C2=A0=C2=A0 Secretary/FAX: +52 614 4391130=C2=A0 =C2= =A0 Lab: +52 614 4394805
E-mail:=C2=A0 daniel.glossman:+:cimav.edu.mx=C2=A0 =C2=A0 =C2=A0 =C2=A0 = =C2=A0 dglossman:+:gmail.com
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2011/8/9 Arthur Doweyko adoweyko%x%comcast.net <owner-chemistry:+:ccl.net>
<= blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px= #ccc solid;padding-left:1ex;">
Sent to CCL by: "Arthur =C2=A0Doweyko" [adoweyko|a|comcast.net]
I'm in the midst of rewriting some old code which made use of the old, = now defunct, Sybyl *.mol file format (not to be confused with the MDL *.mol= format). =C2=A0To this end, does anyone know of an available conversion ut= ility (.mol <--> .mol2), or the location of some example structure fi= les in both formats?
I found an old babel version on CCL, however, it does not run correctly on = my Windows7 platform.
Thanks

-Arthur



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--000325557a620dcf8e04aa19a024-- From owner-chemistry@ccl.net Tue Aug 9 20:49:01 2011 From: "Wolf-D. Ihlenfeldt wdi]![xemistry.com" To: CCL Subject: CCL: AW: old Sybyl *.mol file format Message-Id: <-45234-110809175823-2968-gOj10RHV9tZ2TWi9MXu0wA**server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 9 Aug 2011 23:58:13 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi(~)xemistry.com] The Cactvs toolkit supports both formats. An academic version can be downloaded from www.xemistry.com/academic. If you send me a sample file, I will set up a conversion script for you. > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+wdi==xemistry.com:+:ccl.net [mailto:owner- > chemistry+wdi==xemistry.com:+:ccl.net] Im Auftrag von Arthur Doweyko > adoweyko%x%comcast.net > Gesendet: Dienstag, 9. August 2011 22:12 > An: Ihlenfeldt, Wolf D > Betreff: CCL: old Sybyl *.mol file format > > > Sent to CCL by: "Arthur Doweyko" [adoweyko|a|comcast.net] > I'm in the midst of rewriting some old code which made use of the old, > now defunct, Sybyl *.mol file format (not to be confused with the MDL > *.mol format). To this end, does anyone know of an available > conversion utility (.mol <--> .mol2), or the location of some example > structure files in both formats? > I found an old babel version on CCL, however, it does not run correctly > on my Windows7 platform. > Thanks > > -Arthur> To recover the email address of the author of the message, please > change From owner-chemistry@ccl.net Tue Aug 9 21:24:01 2011 From: "Vincent Leroux vincent.leroux---loria.fr" To: CCL Subject: CCL: old Sybyl *.mol file format Message-Id: <-45235-110809184011-17623-2Tr6dz45KCpQC++q714UaQ,server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 10 Aug 2011 00:39:59 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux,loria.fr] Hi Arthur, You can either use OpenBabel (free) or OpenEye's Babel (free to academics, 1 year-renewable licence). http://openbabel.org http://eyesopen.com Regards VL Le 09/08/11 22:11, Arthur Doweyko adoweyko%x%comcast.net a écrit : > Sent to CCL by: "Arthur Doweyko" [adoweyko|a|comcast.net] > I'm in the midst of rewriting some old code which made use of the old, now defunct, Sybyl *.mol file format (not to be confused with the MDL *.mol format). To this end, does anyone know of an available conversion utility (.mol<--> .mol2), or the location of some example structure files in both formats? > I found an old babel version on CCL, however, it does not run correctly on my Windows7 platform. > Thanks > > -Arthur> > >