From owner-chemistry@ccl.net Fri Feb 6 09:50:01 2015 From: "Syeda Sumayya Tariq sumayyatariq7+*+gmail.com" To: CCL Subject: CCL: How to Customize Box size in Dock 6? Message-Id: <-51006-150206054126-348-/v+xx9bGiZCspVRx/QjS1g###server.ccl.net> X-Original-From: "Syeda Sumayya Tariq" Date: Fri, 6 Feb 2015 05:41:25 -0500 Sent to CCL by: "Syeda Sumayya Tariq" [sumayyatariq7- -gmail.com] Dear All, I am a user of DOCK 6 and am having a little difficulty customizing the box size according to my need. Is there a way to shorten the box size less than 1? I have tried shortening it less than 1 at the showbox step, but it does not seem to make much difference. How can I direct the box at specific site only? Any help would be highly appreciated. Best regards, Syeda Sumayya Tariq Email: sumayyatariq7%%gmail.com From owner-chemistry@ccl.net Fri Feb 6 10:25:01 2015 From: "Renier Dreyer renier.dreyer:+:crunchyard.com" To: CCL Subject: CCL: GAMESS ver 5 Dec 2014 now on CrunchYard Message-Id: <-51007-150206074145-5273-njxQlyXgkExmTJLOxkWSyw|*|server.ccl.net> X-Original-From: "Renier Dreyer" Date: Fri, 6 Feb 2015 07:41:44 -0500 Sent to CCL by: "Renier Dreyer" [renier.dreyer_+_crunchyard.com] CrunchYard is pleased to announce that GAMESS has been updated to version 5 December 2014 on our Cloud based Super Computing facility. Access over 300 true cores (not virtual cores) instantly through our easy to use Web-Site. CrunchYard offers cost effective, user-friendly, secure and reliable engineering simulations online on a pay per use basis. This provides computational chemists around the world the ability to run their own simulations without capital expenses or middle men and no need to manage infrastructure. To start using GAMESS and other software on CrunchYard today, register at www.crunchyard.com or contact Dr Renier Dreyer at +27 11 717-6379, renier.dreyer%%crunchyard.com From owner-chemistry@ccl.net Fri Feb 6 15:06:00 2015 From: "Scott Brozell srb^^osc.edu" To: CCL Subject: CCL: How to Customize Box size in Dock 6? Message-Id: <-51008-150206150313-1546-ScJ0j2iVZL5kIu83rqDaXw]^[server.ccl.net> X-Original-From: Scott Brozell Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Fri, 6 Feb 2015 15:03:01 -0500 Mime-Version: 1.0 Sent to CCL by: Scott Brozell [srb-*-osc.edu] Hi, You will probably get better feedback by posting this on the Dock 6 mailing list: http://mailman.docking.org/mailman/listinfo/dock-fans which can be searched here: http://dock.compbio.ucsf.edu/DOCK_6/index.htm#searchdockfans You may have the sequence of broad steps out of order: Regarding your second question, defining the active site(s) is introduced here: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm where three general options are given for targeting sites. Please clarify your first question; and have you visualized the box (which is for the computational grid) ? scott On Fri, Feb 06, 2015 at 05:41:25AM -0500, Syeda Sumayya Tariq sumayyatariq7+*+gmail. com wrote: > Sent to CCL by: "Syeda Sumayya Tariq" [sumayyatariq7- -gmail.com] > > I am a user of DOCK 6 and am having a little difficulty customizing the box size according to my need. > Is there a way to shorten the box size less than 1? I have tried shortening it less than 1 at the showbox step, but it does not seem to make much difference. How can I direct the box at specific site only? > From owner-chemistry@ccl.net Fri Feb 6 15:40:01 2015 From: "Reed Nieman reed.nieman*o*ttu.edu" To: CCL Subject: CCL:G: Gaussian ListWindow Message-Id: <-51009-150206141911-32117-6NzyMbblia4gixj58wqfRw.@.server.ccl.net> X-Original-From: "Reed Nieman" Date: Fri, 6 Feb 2015 14:19:10 -0500 Sent to CCL by: "Reed Nieman" [reed.nieman,+,ttu.edu] I am having trouble implementing the keyword ListWindow in g09. I am looking to freeze several non-sequential orbitals in a fairly large system and from the documentation at the bottom of this page: http://www.gaussian.com/g_tech/g_ur/k_fc.htm , it looked like it would be exactly what I needed. However, the wording as to how one should use this feature is rather vague and anytime I try to run a test calculation on water freezing orbitals 2 and 4, the output file says that ListWindow is an invalid keyword. The line I use in the input file looks like this (on a single line): #P B3LYP/6-311g* SP pop=reg gfinput gfprint iop(6/7=3) SCF=direct ListWindow=(2 4) I would greatly appreciate any help or guidance with this issue. Best, Reed Nieman reed.nieman- -ttu.edu From owner-chemistry@ccl.net Fri Feb 6 16:15:01 2015 From: "David Deng ddeng ~~ chemaxon.com" To: CCL Subject: CCL: Call for Abstracts: Find the Needle in a Haystack Message-Id: <-51010-150206141922-32153-D7zuo+GS+2jQeIZKLozYSQ+*+server.ccl.net> X-Original-From: "David Deng" Date: Fri, 6 Feb 2015 14:19:21 -0500 Sent to CCL by: "David Deng" [ddeng _ chemaxon.com] Call for Abstracts: Find the Needle in a Haystack: Mining Data from Large Chemical Spaces Organized by David Deng Description: We are now accepting submission of abstracts for consideration for an ACS Division of Chemical Information (CINF) Symposium at the ACS Fall 2015 Meeting in Boston, MA, Aug 16-20, 2015. We live in a time of rapid change. Computer hardware is getting faster and bigger by the minute; software algorithm is becoming smarter; advancement in laboratory technologies allows us to explore new chemical space; scientific literature is being digitalized for easier access... All these improvements has resulted in an exponentially increasing number of scientific data collected. However, this also makes navigating within these databases more and more challenging. This symposium will focus on current challenges and development in dealing with large chemical databases. Related research topics include, but not limited to: 1. Advancement in computer hardware and software for handling large databases, e.g. GPU, parallel computing, etc. 2. Novel search algorithm in large databases, including Markush enumeration and search in chemical patents and combinatorial libraries. 3. Manual and automatic scientific data collection. 4. Curating and validating large databases, to remove incorrect data point and avoid duplicates. 5. Data display and visualization of large databases. 6. Collaboration within the scientific community in dealing with large databases. Format: Oral presentations will be 25-30 minutes, including time for questions. The deadline for submitting an abstract for consideration is March 29th, 2015. Abstracts may be submitted via: http://www.acs.org/content/acs/en/meetings/abstract- submissions/acsnm250/division-of-chemical-information.html Please contact the organizer, David Deng (ddeng#%#chemaxon.com) if you have any questions. From owner-chemistry@ccl.net Fri Feb 6 16:50:01 2015 From: "David Deng cinf.david.deng-#-gmail.com" To: CCL Subject: CCL: Call for Abstracts: Find the Needle in a Haystack: Message-Id: <-51011-150206143254-32644-CdYAzEkq8rfHAkJGi4njlg() server.ccl.net> X-Original-From: "David Deng" Date: Fri, 6 Feb 2015 14:32:53 -0500 Sent to CCL by: "David Deng" [cinf.david.deng:_:gmail.com] Call for Abstracts: Find the Needle in a Haystack: Mining Data from Large Chemical Spaces Organized by David Deng Description: We are now accepting submission of abstracts for consideration for an ACS Division of Chemical Information (CINF) Symposium at the ACS Fall 2015 Meeting in Boston, MA, Aug 16-20, 2015. We live in a time of rapid change. Computer hardware is getting faster and bigger by the minute; software algorithm is becoming smarter; advancement in laboratory technologies allows us to explore new chemical space; scientific literature is being digitalized for easier access... All these improvements has resulted in an exponentially increasing number of scientific data collected. However, this also makes navigating within these databases more and more challenging. This symposium will focus on current challenges and development in dealing with large chemical databases. Related research topics include, but not limited to: 1. Advancement in computer hardware and software for handling large databases, e.g. GPU, parallel computing, etc. 2. Novel search algorithm in large databases, including Markush enumeration and search in chemical patents and combinatorial libraries. 3. Manual and automatic scientific data collection. 4. Curating and validating large databases, to remove incorrect data point and avoid duplicates. 5. Data display and visualization of large databases. 6. Collaboration within the scientific community in dealing with large databases. Format: Oral presentations will be 25-30 minutes, including time for questions. The deadline for submitting an abstract for consideration is March 29th, 2015. Abstracts may be submitted via: http://www.acs.org/content/acs/en/meetings/abstract- submissions/acsnm250/division-of-chemical-information.html Please contact the organizer, David Deng (ddeng^-^chemaxon.com) if you have any questions.