From owner-chemistry@ccl.net Wed Jul 21 08:07:00 2010 From: "Wilfried Langenaeker wilfried.langenaeker(0)silicos.com" To: CCL Subject: CCL:G: Silicos goes Open Source Message-Id: <-42315-100721014934-11380-IwfayYlrblGNboM+Qls+ag _ server.ccl.net> X-Original-From: Wilfried Langenaeker Content-Type: multipart/alternative; boundary=Apple-Mail-1-736454646 Date: Wed, 21 Jul 2010 07:49:25 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Wilfried Langenaeker [wilfried.langenaeker _ silicos.com] --Apple-Mail-1-736454646 Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable PRESS RELEASE: SILICOS NV PORTS ITS PROPRIETARY COMPUTATIONAL CHEMISTRY SOFTWARE INTO =20= THE OPEN SOURCE DOMAIN On June 22, 2010, the Belgium-based computational chemistry company =20 Silicos NV has made a strategic decision to port the majority of its proprietary software =20 into the open source arena. The decision has been made to port all of these tools and the =20 corresponding C/C++ API's into the Open Babel environment under a GNU GPL licensing scheme. This strategic =20 decision will position Silicos NV as one of the leading computational chemistry services =20 companies to support the open source business model. According to Hans De Winter, Silicos' CSO, 'the =20= decision will allow Silicos to move forward rapidly on the expanding wave of open source software =20 tools, and will significantly expand its possibilities of providing services to customers in the =20 pharmaceutical and biotechnological industry.' About Silicos' proprietary software tools Spectrophores=99 are Silicos' patented 3D-field descriptors. =20 Spectrophores=99 are a one-dimensional description of three-dimensional molecular properties, such as atomic =20= electrostatic charges, atomic lipophilicity, atomic softness, atomic electrophilicity and =20 shape. Spectrophores=99 have been succesfully used for clients to build sophisticated QSAR models in =20 combination with many statistical modelling algorithms like bayesian classification and =20 support vector machines. Due to their numeric nature, Spectophores=99 are well-suited for the =20 calculation of self-organising maps. Pharao is Silicos' implementation of a pharmacophore-based alignment =20 tool. It uses a Gaussian representation of pharmacophoric features and generates an alignment =20 between pairs of a set of pharmacophores. The resulting match is quantified using different =20 measures including a Tanimoto coefficient. Piramid is Silicos' software tool incorporating a shape-based =20 alignment between pairs of molecules. Again, the resulting match is quantified using different =20 measures including a Tanimoto coefficient. Finally, Cosmos=99 is Silicos' patented technology for the design of =20 novel molecules using an evolutionary algorithm and using user-specified scoring functions. The =20= tool has been adapted to be used in a fragment-based discovery enviroment. It has been =20 succesfully used in a number of drug discovery programs in which Cosmos=99 was able to generate novel =20= chemistry that has not been described before. The strength of Cosmos=99 lies in its multi-=20 objective optimisation algorithm as well as in the fact that virtually all kinds of scoring functions =20 can be integrated. About Silicos NV Silicos NV is providing services in the field of computational =20 chemistry and virtual screening. The company was founded in 2005 by two former employees of a major =20 pharmaceutical company in Belgium and a former researcher at the ESAT-group of the Catholic =20 University of Louvain. Silicos is a spin-out of the Catholic University of Louvain. For more information For more information regarding Silicos NV, please visit the website at = www.silicos.com=20 or contact Wilfried Langenaeker at +32 478 98 12 20. Silicos NV Wetenschapspark 7 B-3590 Diepenbeek Belgium www.silicos.com --Apple-Mail-1-736454646 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable PRESS = RELEASE: 
SILICOS NV PORTS ITS PROPRIETARY = COMPUTATIONAL CHEMISTRY SOFTWARE INTO THE 
 
On June 22, 2010, the = Belgium-based computational chemistry company Silicos NV has made = a 
strategic decision to port the majority of = its proprietary software into the open source arena. The 
Silicos NV as one of the = leading computational chemistry services companies to support the = open 
source business model. According to Hans = De Winter, Silicos' CSO, 'the decision will allow Silicos = to 
move forward rapidly on the expanding wave = of open source software tools, and will significantly 
biotechnological = industry.' 
 
 
About Silicos' = proprietary software tools 
 
atomic lipophilicity, atomic = softness, atomic electrophilicity and shape. Spectrophores=99 have = been 
succesfully used for clients to build = sophisticated QSAR models in combination with many 
their numeric nature, = Spectophores=99 are well-suited for the calculation of self-organising = maps. 
 
Pharao is = Silicos' implementation of a pharmacophore-based alignment tool. It uses = a Gaussian 
representation of pharmacophoric features = and generates an alignment between pairs of a set of 
coefficient. 
 
Piramid is = Silicos' software tool incorporating a shape-based alignment between = pairs of 
molecules. Again, the resulting match is = quantified using different measures including a Tanimoto 
 
be used in a fragment-based = discovery enviroment. It has been succesfully used in a number = of 
drug discovery programs in which Cosmos=99 = was able to generate novel chemistry that has not 
 
 
About Silicos = NV 
 
Silicos NV is providing = services in the field of computational chemistry and virtual screening. = The 
company was founded in 2005 by two former = employees of a major pharmaceutical company in 
a spin-out of the = Catholic University of Louvain. 
 
For more = information 
 
For more information = regarding Silicos NV, please visit the website at www.silicos.com or = contact 
Wilfried Langenaeker at +32 478 98 12 = 20. 
 
Silicos NV 
B-3590 = Diepenbeek 
Belgium 
www.silicos.com 


= --Apple-Mail-1-736454646-- From owner-chemistry@ccl.net Wed Jul 21 08:42:00 2010 From: "Marat Talipov mirari*o*mail.ru" To: CCL Subject: CCL: visualising NBO in chemcraft Message-Id: <-42316-100720153322-17341-1qTjoH9HG1/tn6GoA4Ur7Q^^server.ccl.net> X-Original-From: Marat Talipov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1251 Date: Wed, 21 Jul 2010 01:33:05 +0600 MIME-Version: 1.0 Sent to CCL by: Marat Talipov [mirari-x-mail.ru] Here is working sample for NBO visualization: --- %mem=100mb %chk=cis.chk #p b3lyp/6-31g(d) scf(tight) pop(nboread,saveNBOs) gfinput gfprint iop(6/7=3) 1 1 O 1.119719000 0.167706000 0.000000000 O 0.000000000 0.513190000 0.000000000 O -1.049378000 -0.508526000 0.000000000 H -0.562727000 -1.378957000 0.000000000 $NBO archive $END --link1-- %mem=100mb %chk=cis.chk #p b3lyp/6-31g(d) guess(read,only) geom(allcheck) iop(6/7=3) gfinput gfprint --- === Sincerely yours, Dr Marat Talipov Research assistant Institute of Organic Chemistry, Ufa Scientific Centre Russian Academy of Sciences From owner-chemistry@ccl.net Wed Jul 21 21:03:00 2010 From: "lamees hegazy lameesshams=yahoo.com" To: CCL Subject: CCL:G: gaussian view and antechamber Message-Id: <-42318-100721202912-27632-H0tu+uaeHM0I1qxhCdz/Pw^_^server.ccl.net> X-Original-From: lamees hegazy Content-Type: multipart/alternative; boundary="0-1835544307-1279758542=:62064" Date: Wed, 21 Jul 2010 17:29:02 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: lamees hegazy [lameesshams!^!yahoo.com] --0-1835544307-1279758542=:62064 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi CCl, I'm trying to build a charged molecule using gaussian view and I don't find= any option which allows me to do that.=20 Also, I'm trying to use mol2 file generated by gaussian view in antechamber= program but antechamber can't read the mol2 file. Does any one has these e= rrors before. =A0 =0A=0A=0A --0-1835544307-1279758542=:62064 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi CCl,

I'm trying to build a charged = molecule using gaussian view and I don't find any option which allows me to= do that.
Also, I'm trying to use mol2 file generated by gaussian view = in antechamber program but antechamber can't read the mol2 file. Does any o= ne has these errors before.

 



=
=0A=0A=0A=0A=0A=0A=0A=0A --0-1835544307-1279758542=:62064-- From owner-chemistry@ccl.net Wed Jul 21 21:38:00 2010 From: "=?iso-8859-1?Q?Gonzalo_Jim=E9nez-Os=E9s?= gonzalo.jimenez . unirioja.es" To: CCL Subject: CCL: HOW TO GET STARTED ON YASARA Message-Id: <-42319-100721202717-27101-+/Nxz4BN9qsQ7Nzo7DWrVA#server.ccl.net> X-Original-From: =?iso-8859-1?Q?Gonzalo_Jim=E9nez-Os=E9s?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 22 Jul 2010 02:26:44 +0200 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?Gonzalo_Jim=E9nez-Os=E9s?= [gonzalo.jimenez() unirioja.es] Hi, Two things: 1) We're not your "guys". We're not your classroom mates, either. At least I'm not. 2) This is (or sometime ago it was) a serious forum. Among the readers of this list are some of the most important personalities in Computational Chemistry (not me, for sure). Please be respectful. Instead of watching the same video for three weeks, just try to read a book on the topic or just follow the old "try & error" strategy until the answer comes. Best wishes, Gonzalo From owner-chemistry@ccl.net Wed Jul 21 23:59:00 2010 From: "Dr Ponnadurai Ramasami ramchemi!A!intnet.mu" To: CCL Subject: CCL: HOW TO GET STARTED ON YASARA Message-Id: <-42320-100721234821-16519-6bMS+wX9iVwceDkLuyeMvw]|[server.ccl.net> X-Original-From: "Dr Ponnadurai Ramasami" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 22 Jul 2010 07:48:10 +0400 MIME-Version: 1.0 Sent to CCL by: "Dr Ponnadurai Ramasami" [ramchemi(0)intnet.mu] Dear CCL Users I strongly agree with Gonzalo. This is professional form. There are many issues that can be addressed with different help services. All the best. Ramasami ----- Original Message -----