From owner-chemistry@ccl.net Mon Jan 6 07:53:00 2014 From: "Prof Ponnadurai Ramasami ramchemi_+_intnet.mu" To: CCL Subject: CCL: Call for abstracts for a Symposium on Computational Chemistry and its Applications-(23-27 June 2014), Mauritius Message-Id: <-49515-140106075027-14512-f7pAhTN6qYC52uv+MfeQCg,server.ccl.net> X-Original-From: "Prof Ponnadurai Ramasami" Content-Language: en-gb Content-Type: multipart/alternative; boundary="----=_NextPart_000_0007_01CF0AFF.64651C80" Date: Mon, 6 Jan 2014 16:50:23 +0400 MIME-Version: 1.0 Sent to CCL by: "Prof Ponnadurai Ramasami" [ramchemi_-_intnet.mu] This is a multipart message in MIME format. ------=_NextPart_000_0007_01CF0AFF.64651C80 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Call for abstracts for a Symposium on Computational Chemistry and its Applications. All topics related to computational chemistry will be considered. The symposium will be part of ICPAC 2014 to be held from 23 to 27 June 2014 in Mauritius. Please visit the website of ICPAC 2014 conference for more details, http://sites.uom.ac.mu/icpac/ Prof Ponnadurai Ramasami, symposium organiser, ramchemi#,#intnet.mu ------=_NextPart_000_0007_01CF0AFF.64651C80 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Call for abstracts for a Symposium on Computational Chemistry and its Applications.

All topics related to computational chemistry will = be considered.

The symposium will be part of ICPAC 2014 to be held = > from 23 to 27 June 2014 in Mauritius.

Please visit the website of ICPAC 2014 conference = for more details, http://sites.uom.ac.mu/icpac/

Prof Ponnadurai Ramasami, symposium organiser, ramchemi#,#intnet.mu

------=_NextPart_000_0007_01CF0AFF.64651C80-- From owner-chemistry@ccl.net Mon Jan 6 11:12:00 2014 From: "Alex Allardyce aallardyce**chemaxon.com" To: CCL Subject: CCL: Flexible small molecule alignment software Message-Id: <-49516-140106071600-11442-sGpDLK6s7hQEu9gfCShCAg(a)server.ccl.net> X-Original-From: Alex Allardyce Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=utf-8 Date: Mon, 6 Jan 2014 13:15:45 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aallardyce(~)chemaxon.com] HI Jian, I forward this link to a recent review published in Drug Discovery. I think it is useful for context but covers and sums some recent relevant developments at ChemAxon, which we are quite proud of. New Approaches to Virtual Screening: http://www.dddmag.com/articles/2013/12/new-approaches-virtual-screening Best wishes for 2014 from an unseasonably, but quite reasonably warm Budapest Alex ----- Original Message ----- > From: "Jian Wang jian.wang---inbox.com" To: "Alex Allardyce " Sent: Friday, January 3, 2014 5:10:19 AM Subject: CCL: Flexible small molecule alignment software Sent to CCL by: "Jian Wang" [jian.wang(0)inbox.com] Hi, happy new year! Can anyone recommend some free software for conformation analysis and flexible alignment of ligands onto a bioactive conformation of reference (or template) molecule? I have some information such as ChemAxon, FieldAlign, etc. And I want to find more. Thanks in advance! Jianhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jan 6 11:47:00 2014 From: "Fedor Goumans goumans(0)scm.com" To: CCL Subject: CCL: Total density from unrestricted ADF calculations Message-Id: <-49517-140106083456-12865-baChLHvtvLK/L7BS2f6aEw ~ server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 06 Jan 2014 14:34:47 +0100 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans a scm.com] Dear Radek, The graphical interface (ADFView) can combine (add, subtract, ...) fields. This uses VTK under the hood, it is not a native option in the densf utility. So, lacking a GUI, you would indeed have to sum the grids manually to get the total density (or subtract them to get spin polarization). Best regards, Fedor On 12/22/2013 3:53 AM, Radoslaw Kaminski rkaminski.rk]_[gmail.com wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk _ gmail.com] > Dear All, > > I was trying to use ADF densf utility to compute the total density from my unrestricted calculations. I used the keyword: > > Density SCF > > This resulted in two CUB files, each with alpha and beta densities. Is there a way to compute one single grid with total density? Obviously I can sum those grids manually, but I would like to produce the total density grid at once. > > Thanks in advance, > > Regards > > Radek> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans() scm.com http://www.scm.com From owner-chemistry@ccl.net Mon Jan 6 13:24:00 2014 From: "Jim Kress ccl_nospam(!)kressworks.com" To: CCL Subject: CCL: Total density from unrestricted ADF calculations Message-Id: <-49518-140106130749-30227-Pw2N6q4E+lZQRme0ftyf7w**server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 6 Jan 2014 13:07:38 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam..:..kressworks.com] You might want to try ChemCraft. I believe it will create and manipulate ADF cube files from ADF output so that you can get the total density. There is a free trial so you might want to try it. http://www.chemcraftprog.com/ Jim -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com.:.ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com.:.ccl.net] On Behalf Of Fedor Goumans goumans(0)scm.com Sent: Monday, January 06, 2014 8:35 AM To: Kress, Jim Subject: CCL: Total density from unrestricted ADF calculations Sent to CCL by: Fedor Goumans [goumans a scm.com] Dear Radek, The graphical interface (ADFView) can combine (add, subtract, ...) fields. This uses VTK under the hood, it is not a native option in the densf utility. So, lacking a GUI, you would indeed have to sum the grids manually to get the total density (or subtract them to get spin polarization). Best regards, Fedor On 12/22/2013 3:53 AM, Radoslaw Kaminski rkaminski.rk]_[gmail.com wrote: > Sent to CCL by: "Radoslaw Kaminski" [rkaminski.rk _ gmail.com] Dear > All, > > I was trying to use ADF densf utility to compute the total density from my unrestricted calculations. I used the keyword: > > Density SCF > > This resulted in two CUB files, each with alpha and beta densities. Is there a way to compute one single grid with total density? Obviously I can sum those grids manually, but I would like to produce the total density grid at once. > > Thanks in advance, > > Regards > > Radek> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans|-|scm.com http://www.scm.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Jan 6 14:12:00 2014 From: "mahnaz gh mahnaz271163%a%yahoo.com" To: CCL Subject: CCL: SCF energy Message-Id: <-49519-140106141102-20113-eqbexNY9/giggKLUfHlBDg+*+server.ccl.net> X-Original-From: "mahnaz gh" Date: Mon, 6 Jan 2014 14:11:00 -0500 Sent to CCL by: "mahnaz gh" [mahnaz271163 _ yahoo.com] hi there I have a molecule which have two different structure in acidic or neutral conditions. In order to determine which of them is the more stable structure, I used the SCF done term, the values is as follows: SCF done 1 = -1330.29275098 and SCF done 2 = -1330.76227822. Could you please help me and tell which of them is the more stable one and is the difference enough to distinguish between the structures? Regards