From owner-chemistry@ccl.net Mon Nov 10 04:11:01 2008 From: "Andrew Dalke dalke _ dalkescientific.com" To: CCL Subject: CCL: Problems with NAMD simulations Message-Id: <-38067-081110033612-23521-iXH4V+QaTDAONuI3Y3NDpw-#-server.ccl.net> X-Original-From: Andrew Dalke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 10 Nov 2008 09:35:56 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Andrew Dalke [dalke-#-dalkescientific.com] Hello Marcus, On Nov 9, 2008, at 8:55 PM, Marcus Vinicius Batista genetics.marcus,gmail.com wrote: > Hi everyone, I am with a problem with NAMD software and I hope > anyone could help me. When I type in the Terminal Window "namd2 ubq > ws eq.conf > ubq ws eq.log" to run my simulation, en error message > occur: unable to open charmm parameter file. However, the file > seems to be ok. I don't know what to do, I hope someone could help me. Try contacting the NAMD mailing list; http://www.ks.uiuc.edu/Research/namd/mailing_list/ They would be able to give you better diagnostics. You should also include more details about the reported error, including a copy&paste of the full error message you got. For example, the source code has: sprintf(err_msg, "UNABLE TO OPEN CHARMM PARAMETER FILE %s\n", fname); NAMD_die(err_msg); which means you should also report the filename it gave and some verification (like an "ls -l") that the file exists and has the right permissions. As an advanced topic, if you had to figure things out from scratch, use "strace" or the equivalent for your OS. This would show exactly which files NAMD was trying to open, and you could see if it was looking in the wrong directory or if there were permission errors. Andrew dalke[#]dalkescientific.com -- Consulting and training in software development for cheminformatics. Next Python training sessions: Dec 4-5, 2008 (San Francisco), 2-4 March (Leipzig) http://dalkescientific.com/training/ From owner-chemistry@ccl.net Mon Nov 10 07:22:00 2008 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas#,#chem.elte.hu" To: CCL Subject: CCL:G: Relaxed scan using GDIIS with Gaussian Message-Id: <-38068-081110061424-29805-EYidVbh2FcQ+02v1KhdDCQ ~~ server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Fri, 07 Nov 2008 12:18:05 +0000 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas:_:chem.elte.hu] Hi Guanna, The other dihedrals around bond N2 N3 may prevent the change of dihedral N1 N2 N3 N4 due to redundancy. One dihedral is usually enough to describe a torsion around a bond and it can be that single dihedral which is intended to scan. Best wishes, Odon On Fri, 2008-11-07 at 19:22 +0800, gnli gnli##dicp.ac.cn wrote: > Sent to CCL by: "gnli" [gnli,+,dicp.ac.cn] > Why it need to add the line "* N2 N3 * R"? > Isn't the purpose scan the N1 N2 N3 N4 ? > Thank you for a explanation! > > best wishes > Guanna Li > gnli|a|dicp.ac.cn > > > > > > > -----Original Message----- > > From: owner-chemistry|a|ccl.net [mailto:owner-chemistry|a|ccl.net] > Sent: Friday, November 07, 2008 4:33 PM > To: Li, Guanna > Subject: CCL:G: Relaxed scan using GDIIS with Gaussian > > > Sent to CCL by: "Jose Pedro Ceron" [jpceron:um.es] > Dear Gianluca, > > You only have to include in calculation route the Modredundant keyword > instead of Z-matrix. In the case of dihedral dih9=N1-N2-N3-N4 your input > should be: > > #P PM3 opt=(tight,gdiis,modredundant) gfinput gfprint IOP(6/7=3) pop=full > > Then Z-matrix and geometrical parameters. > (Blank line) > * N2 N3 * R > N1 N2 N3 N4 0.000 S 35 10.0 > > You have more information in G03 Manual, Opt keyword, Relaxed Potential > Energy. > And that's all. I hope this helps you. > > Jose P. Ceronhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- > No virus found in this incoming message. > Checked by AVG. > Version: 7.5.549 / Virus Database: 270.9.0/1772 - Release Date: 2008-11-6 > 20:23> > -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Mon Nov 10 08:57:01 2008 From: "him demon himadri.de/a\gmail.com" To: CCL Subject: CCL:G: Gaussian98 - ECP Message-Id: <-38069-081110030336-25066-RWKj02jiPZ3G/o7kteHi1A..server.ccl.net> X-Original-From: "him demon" Date: Mon, 10 Nov 2008 03:03:32 -0500 Sent to CCL by: "him demon" [himadri.de]~[gmail.com] Dear Friends, I am interested in trying out some ECP and relativistric ECP calculations on Au systems in Gaussian 98W. I had been trying it for quite sometime but absolutely hav no clues how to put the ECP cards in the input, apart from the existing basis sets in the program. Can someone please help how to build the input ? From owner-chemistry@ccl.net Mon Nov 10 11:05:01 2008 From: "Nancy Neale nealen/./mail.nih.gov" To: CCL Subject: CCL:G: Gaussian98 - ECP Message-Id: <-38070-081110110303-10450-T74XnrkTPyYOe6E5XTmiHQ.:.server.ccl.net> X-Original-From: "Nancy Neale" Date: Mon, 10 Nov 2008 11:02:59 -0500 Sent to CCL by: "Nancy Neale" [nealen*|*mail.nih.gov] Here is an example of an input file I used for a job on a Tb complex: %chk=filename %mem=60MW %nproc=4 # opt=noraman rhf/genecp freq guess=(nosymm,huckel) geom=connectivity Title line 0 1 N Tb 38 B86 36 A85 33 D84 0 1 ! Defining basis sets for atoms H 0 6-31g(d,p) **** C 0 6-31g(d,p) **** N 0 6-31g(d,p) **** O 0 6-31g(d,p) **** ! This is the basis set for the lanthanide ! (7s6p5d)/[5s4p3d]-Basissatz fuer PP. von Ref 11. Tb 0 S 3 1.00 7.7447900 -0.2690350 6.7188320 0.6071530 2.7444700 -1.2912950 S 1 1.00 0.6551160 1.0 S 1 1.00 0.3225940 1.0 S 1 1.00 0.0598710 1.0 S 1 1.00 0.0278300 1.0 P 3 1.00 4.8538560 0.2091380 3.4071410 -0.5624610 0.8065500 1.1805410 P 1 1.00 0.3469710 1.0 P 1 1.00 0.1103260 1.0 P 1 1.00 0.0364430 1.0 D 3 1.00 2.5170570 -0.0528310 0.9211490 0.3620900 0.3716970 0.7321190 D 1 1.00 0.1421020 1.0 D 1 1.00 0.0526750 1.0 ! References: ! [11] M. Dolg, H. Stoll, A. Savin, H. Preuss, Theor. Chim. Acta 75, 173 (1989). **** ! this is the pseudopotential for the lanthanide ! Q=11., MEFIT, WB, Ref 18, Ref 11. Tb 0 ECP54MWB,4,54 G-Komponente 1 2 1.000000 0.000000 S-G 2 2 5.326000 139.661156 2 2.663000 -5.767915 P-G 2 2 4.559800 79.049864 2 2.279900 1.864568 D-G 2 2 3.170700 35.140886 2 1.585400 0.879040 F-G 1 2 6.525900 -80.073275 ! References: ! [11] M. Dolg, H. Stoll, A. Savin, H. Preuss, Theor. Chim. Acta 75, 173 (1989). ! [18] M. Dolg, H. Stoll, H. Preuss, Theor. Chim. Acta 85, 441 (1993). The lines with the ! before them are comment lines. Both the basis set and the pseudopotential were obtained from the Stuttgart group: http://www.theochem.uni-stuttgart.de/pseudopotentials/clickpse.en.html I hope this helps. Regards, Nancy Neale >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Sent to CCL by: "him demon" [himadri.de]~[gmail.com] Dear Friends, I am interested in trying out some ECP and relativistric ECP calculations on Au systems in Gaussian 98W. I had been trying it for quite sometime but absolutely hav no clues how to put the ECP cards in the input, apart from the existing basis sets in the program. Can someone please help how to build the input ? From owner-chemistry@ccl.net Mon Nov 10 12:40:01 2008 From: "Brunsteiner, Michael micb+/-uic.edu" To: CCL Subject: CCL: Two not-so-related questions Message-Id: <-38071-081108230158-15266-HGhDA9FU0WDpUE+4hnELzg_+_server.ccl.net> X-Original-From: "Brunsteiner, Michael" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sat, 8 Nov 2008 21:01:45 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: "Brunsteiner, Michael" [micb-#-uic.edu] On Sat, November 8, 2008 14:23, Joe Leonard jleonard42(!)gmail.com wrote: > > Sent to CCL by: Joe Leonard [jleonard42]_[gmail.com] > Folks, I've been trying to google for answers for these two questions, > but it is a bit like drinking from a fire hose. Therefore, I thought > I'd ask CCL's readers in the hope that they are doing work or are > aware of work in these areas: > > 1. Has there been publications relating the electrostatic potential of > a molecule to its pharmacophore points (h-bond donor/acceptor)? This > would be a useful relation of calculated/theoretical information with > classical/2D-search(rule) based properties. Such a relation would > provide a nice handle on substituent effects not easily modeled via > rules. not sure whether this is what you want, but did you consider COMFA (comparative molecular field analysis) or COMSIA? From owner-chemistry@ccl.net Mon Nov 10 14:30:01 2008 From: "Janjua Ramzan Saeed janjua]^[nenu.edu.cn" To: CCL Subject: CCL: DOS Density of States ?? Message-Id: <-38072-081110120926-10667-nqkkuvMI1L6HN5S86lO+2Q*o*server.ccl.net> X-Original-From: "Janjua Ramzan Saeed" Date: Mon, 10 Nov 2008 12:09:22 -0500 Sent to CCL by: "Janjua Ramzan Saeed" [janjua()nenu.edu.cn] Hi ! I want to know that how can we calculate DOS (density of states) by using ADF software? Janjua PhD Scholar Northeast Normal University, Changchun, CHINA From owner-chemistry@ccl.net Mon Nov 10 19:10:00 2008 From: "Andrew Orry orry.molsoft#gmail.com" To: CCL Subject: CCL: Protein Structure and Drug Design Workshop - MolSoft February 5-6 2009 Message-Id: <-38073-081110190630-20281-sR7aJxqWE69zAeRO9RrZnw::server.ccl.net> X-Original-From: Andrew Orry Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 10 Nov 2008 16:08:36 -0800 MIME-Version: 1.0 Sent to CCL by: Andrew Orry [orry.molsoft*_*gmail.com] **MolSoft ICM Workshop: "Protein Structure and Drug Discovery" February 5th to 6th 2009 La Jolla, CA.** Please see the following invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on February 5th to 6th 2009 in La Jolla, California USA. Please see www.molsoft.com/training.html for more information and a registration form. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft). The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, Chemical Clustering, Searching, Superposition etc... - QSAR, Machine Learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D Ligand Editor - design and optimize ligands interactively - Markush Library Docking - Multiple Receptor Docking (A method to incorporate receptor flexibility) - Automated model building into electron density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing molecular movie making "The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy*molsoft.com or call (858) 625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Latest Newsletter: http://www.molsoft.com/news.html MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com