From owner-chemistry@ccl.net Tue Jun 23 06:22:00 2009 From: "Jose R. Valverde jrvalverde * cnb.csic.es" To: CCL Subject: CCL: Docking free software Message-Id: <-39596-090623034600-9438-Y56+/AWJmGoqsypHUpzYFQ~~server.ccl.net> X-Original-From: "Jose R. Valverde" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 23 Jun 2009 08:47:42 +0200 Mime-Version: 1.0 Sent to CCL by: "Jose R. Valverde" [jrvalverde=-=cnb.csic.es] There are many options available, try these - GRAMM - 3D-Dock - Autodock a search for any of them will take you to their home pages. Some even have a web interface to run them for free. Speaking of which there are several web servers providing protein-protein docking for free. A cursory search should get you pointers to them. j On Mon, 22 Jun 2009 10:37:54 +0430 "Babak Khalili khalili.babak+/-gmail.com" wrote: > > Sent to CCL by: Babak Khalili [khalili.babak(-)gmail.com] > Dear subscribers, > > I have to dock 2 peptides together, may you help me to find some free > software and a procedure, also. > > Tank you in advance, > Babak Khalili, > PhD candidate of biochemistry > -- EMBnet/CNB Scientific Computing Service Solving all your computer needs for Scientific Research. http://bioportal.cnb.csic.es http://www.es.embnet.org From owner-chemistry@ccl.net Tue Jun 23 12:02:00 2009 From: "Yong Yan yanyongwhu]=[yahoo.com" To: CCL Subject: CCL:G: how to figure out the symmetry of MOs Message-Id: <-39597-090622170619-22374-W/BwuGD2N3j0tWThM3hSEg[a]server.ccl.net> X-Original-From: "Yong Yan" Date: Mon, 22 Jun 2009 17:06:15 -0400 Sent to CCL by: "Yong Yan" [yanyongwhu*|*yahoo.com] Hi, Dear All; I just do not know how to figure out the symmetry of each molecular orbitals from G03. All the symmetries are "C1" and each MO symmetry is "A" instead in Webmo(which is the lowest point group). But I am really trying to know how to generate the Mulliken symbols for MOs around frontier MO. Thank you very much for you helps! Yong Yan Chemistry Tulane Univ. yanyongwhu ~ yahoo.com From owner-chemistry@ccl.net Tue Jun 23 12:38:01 2009 From: "Yong Yan yanyongwhu===yahoo.com" To: CCL Subject: CCL:G: symmetry of Melcualr orbitals Message-Id: <-39598-090623105219-8212-5tBYLYcZd0BnUHkvkyUIfg(!)server.ccl.net> X-Original-From: "Yong Yan" Date: Tue, 23 Jun 2009 10:52:15 -0400 Sent to CCL by: "Yong Yan" [yanyongwhu[A]yahoo.com] Hi, Dear All; I just do not know how to figure out the symmetry of each molecular orbitals from G03. All the symmetries are "C1" and each MO symmetry is "A" instead in Webmo(which is the lowest point group). But I am really trying to know how to generate the Mulliken symbols for MOs around frontier MO. Thank you very much for you helps! Yong Yan Chemistry Tulane Univ. yanyongwhu^-^yahoo.com From owner-chemistry@ccl.net Tue Jun 23 13:14:01 2009 From: "yarasi rao gnsmmg * yahoo.com" To: CCL Subject: CCL: gar2ped Message-Id: <-39599-090623000540-22382-WT59BJ7dlYHA+Z4ZGdYi7A[A]server.ccl.net> X-Original-From: "yarasi rao" Date: Tue, 23 Jun 2009 00:05:36 -0400 Sent to CCL by: "yarasi rao" [gnsmmg(_)yahoo.com] I downloaded gar2ped from ccl.net. After compiling two executable, pullarc and gar2ped.x were created. Though pullarc is working the command to run gar2ped.x to generate *.apt.xyz, nomos.xyz and nomo.nn.xyz is not working. I am not able to run this command even for test file, triazine.arch given in the program.. Can I have help in this regards thanks Yarasi From owner-chemistry@ccl.net Tue Jun 23 13:48:00 2009 From: "Mr. Wang Long mr.wang.long%gmail.com" To: CCL Subject: CCL: A question on excited state optimization Message-Id: <-39600-090623070336-10864-/ZbNOpqCyYI5P2UCF4uNiA{=}server.ccl.net> X-Original-From: "Mr. Wang Long" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 23 Jun 2009 18:56:05 +0800 MIME-Version: 1.0 Sent to CCL by: "Mr. Wang Long" [mr.wang.long~!~gmail.com] Hi, I'm trying to run an excited state optimization with PCGamess but failed. This is my input file: $CONTRL SCFTYP=RHF DFTTYP=BLYP CITYP=TDDFT RUNTYP=optimize $END $SYSTEM TIMLIM=3000 MEMORY=3000000 $END $BASIS GBASIS=n31 ngauss=6 NDFUNC=1 $END $TDDFT NSTATE=3 ISTSYM=0 ISTATE=1 $END $DATA H2O CNV 2 O 8.0 0.0000000000 0.0000000000 0.7205815395 H 1.0 0.0000000000 0.7565140024 0.1397092302 $END I found this error message in output file: "TDHF&TDDFT gradient are not yet programmed". But I googled and found many people saying that PCGamess is able to perform excited state optimization. Are there any extra keywords required? Is Gamess-US able to run this kind of job? Thanks! Wang Long