From owner-chemistry@ccl.net Mon Mar 9 01:20:00 2009 From: "Brunsteiner, Michael micb{=}uic.edu" To: CCL Subject: CCL: MM-PBSA calculation in Gromacs Message-Id: <-38799-090308212717-8364-IhCkAlT4jLoABb9QFowPwg * server.ccl.net> X-Original-From: "Brunsteiner, Michael" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 8 Mar 2009 20:27:06 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: "Brunsteiner, Michael" [micb{=}uic.edu] On Sun, March 8, 2009 18:58, Neha Gandhi n.gandhiau..gmail.com wrote: > > Sent to CCL by: Neha Gandhi [n.gandhiau^gmail.com] > Hi, > > Did anyone tried running mm-pbsa using gromacs trajectories? Are there > any scripts to run mm-pbsa calculations in gromacs? I've used gromacs+ffamber+apbs. but there is no script that does all the work out-of-the box, you need to generate input and analyze output for the various programs, which is straightforward to do with awk, python, or the like ... but be aware that MMPBSA results are VERY sensitive to the parameters such as Born radii partial charges and the interior dielectric constant. so before you perform any extensive calculations you want to make sure that MMPBSA gives you the right answers with your choice of parameters and for your system. mic From owner-chemistry@ccl.net Mon Mar 9 04:06:01 2009 From: "Joannis Apostolakis apostola . bio.ifi.lmu.de" To: CCL Subject: CCL: Chil2 plattform for molecular modelling Message-Id: <-38800-090309035941-24767-IAgnd2A2Q0yBfuQHGnanKQ*server.ccl.net> X-Original-From: Joannis Apostolakis Content-Type: multipart/mixed; boundary="------------060701010301030605020008" Date: Mon, 09 Mar 2009 08:59:25 +0100 MIME-Version: 1.0 Sent to CCL by: Joannis Apostolakis [apostola---bio.ifi.lmu.de] This is a multi-part message in MIME format. --------------060701010301030605020008 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Short correction: The link below should read www.chil2.de. I apologize for the mistake and the reposting. With best regards Jannis joannis_98]*[yahoo.com wrote: > Dear Colleagues, this is to announce that the Chil2 platform > containing a number of high quality > tools for molecular modelling, design and cheminformatics is available > at the > site www.chli2.de. For academics it is free of charge and can be used > on an > unlimited number of cpus. It comes with a license that expires every > three > months, and which can then be renewed by downloading it again from the > site. Companies are welcome to test for the same period of time under > the same > conditions, however will need to buy the license for use beyond the > first three > months. > Chil2 contains GlamDock, a highly efficient and accurate protein > ligand docker (Tietze and > Apostolakis 2007, JCIM) GMA possibly the fastest flexible structural > alignment approach (Marialke et > al. 2007, JCIM) > HomDock a structure/ligand based docking alignment tool for fast > docking of > ligands that are similar to a given target. (Marialke et al. 2008) > FUZZEE, a weighted reduced graph similarity approach that allows in > the order > of 1000 molecule comparisons per second and a simple library viewer > that allows scrolling through screening results and > viewing of the relevant structures. > Chil2 is written in JAVA and is therefore largely system independent. > We believe the platform is an interesting addition to the existing > repertoire > of methods and are looking forward to your feedback. > With best regards Jannis Apostolakishttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > > -- Dr. Joannis Apostolakis Tel.: ++49 89 2180 40 57 Fax.: ++49 89 2180 99 40 57 http://www.bio.ifi.lmu.de/~apostola http://www.chil2.de -- Dr. Joannis Apostolakis Tel.: ++49 89 2180 40 57 Fax.: ++49 89 2180 99 40 57 http://www.bio.ifi.lmu.de/~apostola http://www.chil2.de --------------060701010301030605020008 Content-Type: text/x-vcard; charset=utf-8; name="apostola.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="apostola.vcf" begin:vcard fn:Dr. Joannis Apostolakis n:Apostolakis;Dr. Joannis email;internet:apostola]*[bio.ifi.lmu.de tel;work:++49 89 2180 40 57 tel;fax:++49 89 2180 99 4057 url:http://www.chil2.de version:2.1 end:vcard --------------060701010301030605020008-- From owner-chemistry@ccl.net Mon Mar 9 08:11:01 2009 From: "Maura Mooney mmooney05||qub.ac.uk" To: CCL Subject: CCL: NX Disabled Message-Id: <-38801-090309080924-7264-XnHnDmaKnB/kXR+85E3e3w]^[server.ccl.net> X-Original-From: "Maura Mooney" Date: Mon, 9 Mar 2009 08:09:20 -0400 Sent to CCL by: "Maura Mooney" [mmooney05#qub.ac.uk] Hi all, Recently I have installed NX on my Dell Ubuntu machine. I have had no problem using it (to connect from my XP-Pro to my Dell-Ubuntu), but when I attempted to use it last week it reported the following error: The NX service is not available or the NX access was disabled on host xxx.xxx.xxx.xxx (the IP) I attempted to restart the nxserver but this was unsuccessful. I would be most grateful for any advice (as I can't work from home ) Cheers, Maura (mmooney05^qub.ac.uk) From owner-chemistry@ccl.net Mon Mar 9 13:33:00 2009 From: "Conley, Michael mconley#%#leadscope.com" To: CCL Subject: CCL: FDA QSAR Models Available at SOT Conference in Baltimore Maryland Message-Id: <-38802-090309114542-1570-8RhzcKNqo5QOw5NTZoFqTg .. server.ccl.net> X-Original-From: "Conley, Michael" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C9A0C9.8BA0AB75" Date: Mon, 9 Mar 2009 11:13:04 -0400 MIME-Version: 1.0 Sent to CCL by: "Conley, Michael" [mconley|-|leadscope.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C9A0C9.8BA0AB75 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 TGVhZHNjb3BlIGFubm91bmNlcyB0aGUgYXZhaWxhYmlsaXR5IG9mIHRoZSBMZWFkc2NvcGUgRkRB IE1vZGVsIEFwcGxpZXIgKFFTQVIgTW9kZWxzKS4gIElmIHlvdSBhcmUgYXR0ZW5kaW5nIHRoZSBT 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bj48L2ZvbnQ+PC9wPg0KDQo8L2Rpdj4NCg0KPC9ib2R5Pg0KDQo8L2h0bWw+DQo= ------_=_NextPart_001_01C9A0C9.8BA0AB75-- From owner-chemistry@ccl.net Mon Mar 9 16:04:01 2009 From: "Andrew Dalke dalke[#]dalkescientific.com" To: CCL Subject: CCL: Python training in cheminformatics, Leipzig, 27-29 April Message-Id: <-38803-090309143404-25912-ofpkhNDYzxiXdESuqv+NBA[a]server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Mon, 9 Mar 2009 11:33:50 -0600 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Andrew Dalke [dalke-,-dalkescientific.com] My next training course on Python for cheminformatics will be in Leipzig, Germany on 27-29 April. For full details see http://dalkescientific.com/training/ The schedule for the three day course is Day 1: overview of Python and OEChem, Day 2: plotting with matplotlib, communicating with Excel, XML processing, subprocess, NumPy and R. Day 3: SQL databases and web development with Django. The course is designed for working computational chemists who know how to do some programming and want more training in how to use Python effectively for their research. The examples and hands-on exercises are all drawn > from cheminformatics. If you have any questions or to register, please contact me. Andrew dalke]~[dalkescientific.com From owner-chemistry@ccl.net Mon Mar 9 20:29:00 2009 From: "Esteban Gabriel Vega Hissi egvega%a%gmail.com" To: CCL Subject: CCL:G: Gaussian g2mp2 error Message-Id: <-38804-090309193045-9114-UNCu3teik5eooyGJba7PJg/a\server.ccl.net> X-Original-From: "Esteban Gabriel Vega Hissi" Date: Mon, 9 Mar 2009 19:30:41 -0400 Sent to CCL by: "Esteban Gabriel Vega Hissi" [egvega[A]gmail.com] Hi everyone, I hope any of you can help me with this: I'm performing a g2mp2 calculation on gaussian 03 and I get this error: Disk-based method using ON**2 memory for 40 occupieds at a time. Estimated scratch disk usage= -1 words. Inconsistency from DE2Siz in DoE2D. Error termination via Lnk1e in /extra//g03/l906.exe at Mon Mar 9 16:13:07 2009. May be a memory problem? I use this in my input file: %chk=half.chk %mem=40MW %nproc=1 %rwf=r1,2GB,r2,2GB,r3,2GB,r4,2GB,r5,2GB,r6,2GB,r7,2GB,r8,2GB,r9,2GB,r10,2GB,r11, 2GB,r12,2GB,r13,2GB,r14,2GB,r15,2GB # g2mp2 MaxDisk=30GB Thanks in advance! Esteban Gabriel Vega Hissi UNSL Argentina