From owner-chemistry@ccl.net Mon Jun 15 10:30:00 2015 From: "Rene Thomsen rene.thomsen_-_qiagen.com" To: CCL Subject: CCL: Distribution of MMFF94 parameter files Message-Id: <-51445-150615101857-30431-MEAxJg+sxvq2MVgktdvekA_._server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 15 Jun 2015 10:18:56 -0400 Sent to CCL by: "Rene Thomsen" [rene.thomsen^qiagen.com] Hi, I have a few questions regarding distribution of MMFF94 parameter files. Dr. Simon Kearsley is listed as the contact person on the MMFF94s Validation Suite webpage ( http://www.ccl.net/cca/data/MMFF94s/). Unfortunately, I have not been able to get in touch with Simon via email or LinkedIn. Is there anyone here who know whether he is still the contact person regarding MMFF94 issues? Kind regards, Rene --- Rene Thomsen Senior Scientific Developer QIAGEN Aarhus Silkeborgvej 2, Prismet DK-8000 Aarhus C www.clcbio.com rene.thomsen|a|qiagen.com From owner-chemistry@ccl.net Mon Jun 15 14:51:00 2015 From: "Joseph Leonard jleonard42-*-gmail.com" To: CCL Subject: CCL: Distribution of MMFF94 parameter files Message-Id: <-51446-150615144136-10003-6DsC0J2jTMrjqV0pAQGQDQ-,-server.ccl.net> X-Original-From: Joseph Leonard Content-Type: text/plain; charset=UTF-8 Date: Mon, 15 Jun 2015 14:41:31 -0400 MIME-Version: 1.0 Sent to CCL by: Joseph Leonard [jleonard42|,|gmail.com] Hmm... Not sure anybody still maintains this stuff. Tom Halgren went from Merck to Schrodinger and I assume he's retired from there. Simon left Merck a while back and I'm not sure where he ended up. Perhaps somebody at Merck might be looking after this, but there's a chance it's "frozen in time" and avail on CCL as is? What do you need re: this? Joe On Mon, Jun 15, 2015 at 10:18 AM, Rene Thomsen rene.thomsen_-_qiagen.com wrote: > > Sent to CCL by: "Rene Thomsen" [rene.thomsen^qiagen.com] > Hi, > > I have a few questions regarding distribution of MMFF94 parameter files. > > Dr. Simon Kearsley is listed as the contact person on the MMFF94s Validation Suite webpage ( > http://www.ccl.net/cca/data/MMFF94s/). > > Unfortunately, I have not been able to get in touch with Simon via email or LinkedIn. > Is there anyone here who know whether he is still the contact person regarding MMFF94 issues? > > Kind regards, > Rene > --- > Rene Thomsen > Senior Scientific Developer > > QIAGEN Aarhus > Silkeborgvej 2, Prismet > DK-8000 Aarhus C > > www.clcbio.com > rene.thomsen__qiagen.com> > -- For those scoring at home, 'judicial activism' is when a court issues a ruling you don't like. From owner-chemistry@ccl.net Mon Jun 15 17:14:00 2015 From: "Lela Vukovic Lvukov1^^illinois.edu" To: CCL Subject: CCL: Simulation Based Drug Discovery Workshop, San Diego, Sept 21-25, 2015 Message-Id: <-51447-150615163927-19675-lpRQCuaQAG0QhC413CUmYA[-]server.ccl.net> X-Original-From: "Lela Vukovic" Date: Mon, 15 Jun 2015 16:39:26 -0400 Sent to CCL by: "Lela Vukovic" [Lvukov1..illinois.edu] The National Biomedical Computation Resource (NBCR) (http://nbcr.ucsd.edu/wordpress2/) at the University of California San Diego (www.ucsd.edu) and the Theoretical and Computational Biophysics Group (TCBG), NIH Resource for Macromolecular Modeling and Bioinformatics (www.ks.uiuc.edu) at the University of Illinois at Urbana-Champaign (www.uiuc.edu) are pleased to offer a joint workshop on the theme of molecular simulation and small molecule drug discovery: Simulation Based Drug Discovery Workshop http://www.ks.uiuc.edu/Training/Workshop/SanDiego2015/ to be held September 21-25, 2015 at the University of California San Diego. Application, selection, and notification of participants is on-going through August 20, 2015; deadline for applications is August 1, 2015. The intensive program will introduce 12-25 students to principles, methods, and NBCR / TCBG tools for simulating receptors (globular and membrane bound), small molecule docking, rigorous free energy calculations, and drug discovery strategies and workflows. The workshop is designed for graduate students, and postdoctoral and other researchers interested in computational drug discovery. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations. Those accepted into the program will be encouraged to bring and work with their own drug targets. All participants are required to bring their own laptop, prepared for use in workshop tutorial sessions. Course materials will be provided. Workshop slots are limited and available on a first-come, first-serve basis. Women and underrepresented students are strongly encouraged to apply. The workshop is sponsored by the National Institute of General Medical Sciences (www.nigms.nih.gov) and the NIH Center for Macromolecular Modeling and Bioinformatics. We look forward to receiving your application! TCBG Workshop Organizers Email: workshop+sandiego2015]=[ks.uiuc.edu From owner-chemistry@ccl.net Mon Jun 15 19:30:01 2015 From: "Michael K. Gilson mgilson~!~ucsd.edu" To: CCL Subject: CCL: Open source AMBER Tools distribution of Grid Inhomogeneous Solvation Theory (GIST) for analysis of water structure and thermodynamics Message-Id: <-51448-150615190745-24413-2UvDrg0i7aOu/RjGoAbwNw=-=server.ccl.net> X-Original-From: "Michael K. Gilson" Content-Type: multipart/alternative; boundary="------------040900010301000007000202" Date: Mon, 15 Jun 2015 16:07:27 -0700 MIME-Version: 1.0 Sent to CCL by: "Michael K. Gilson" [mgilson,+,ucsd.edu] This is a multi-part message in MIME format. --------------040900010301000007000202 Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 7bit Dear CCL Colleagues, This is to let you know that software to analyze the structure and thermodynamics of water at protein and other surfaces is now freely available as part of the open-source AMBER Tools package. The method, called Grid Inhomogeneous Solvation Theory, uses the same underlying theory as WaterMap but generates 3D grids of water properties, rather than focusing on discrete hydration sites. The software is integrated into cpptraj, and is available here: http://ambermd.org/AmberTools14-get.html The GIST functionality is detailed in the user manual, and a detailed tutorial is available here: http://ambermd.org/tutorials/ The main reference article is here: http://scitation.aip.org/content/aip/journal/jcp/137/4/10.1063/1.4733951 We hope you find this useful. Feel free to contact us if you have any questions. Regards, Mike Gilson UCSD Tom Kurtzman Lehman College, CCNY --------------040900010301000007000202 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit Dear CCL Colleagues,

This is to let you know that software to analyze the structure and thermodynamics of water at protein and other surfaces is now freely available as part of the open-source AMBER Tools package.  The method, called Grid Inhomogeneous Solvation Theory, uses the same underlying theory as WaterMap but generates 3D grids of water properties, rather than focusing on discrete hydration sites. 
The software is integrated into cpptraj, and is available here: http://ambermd.org/AmberTools14-get.html  

The GIST functionality is detailed in the user manual, and a detailed tutorial is available here: http://ambermd.org/tutorials/
The main reference article is here: http://scitation.aip.org/content/aip/journal/jcp/137/4/10.1063/1.4733951
We hope you find this useful. Feel free to contact us if you have any questions.

Regards,

Mike Gilson
UCSD

Tom Kurtzman
Lehman College, CCNY

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