From chemistry-request@server.ccl.net Sat Oct 12 12:23:35 2002 Received: from nbcs-av3.rutgers.edu ([128.6.72.254]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9CGNZB31311 for ; Sat, 12 Oct 2002 12:23:35 -0400 Received: from er4.rutgers.edu(165.230.180.142) by nbcs-av3.rutgers.edu via csmap id 23807; Sat, 12 Oct 2002 12:25:08 -0400 (EDT) Received: by eden.rutgers.edu (Postfix, from userid 37805) id 0C332B022; Sat, 12 Oct 2002 15:46:57 +0000 (US/Eastern) Date: Sat, 12 Oct 2002 11:46:57 -0400 (EDT) From: Jianquan Chen X-X-Sender: jianquan@er4.rutgers.edu To: chemistry@ccl.net Subject: stack size in the Mac OS X (Autodock3) In-Reply-To: <200210091826.LAA01653@haney.hbond.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I met a strange problem when I run AutoDock3 in the MAC OS X. my os version is 10.1.5. I increased the max atom types in autodock3. after compilation, I ran it, but it failed. the error message was segmentation fault. I typed the command "limit stacksize unlimited; limit" it showed now the maximal stacksize was 65536k bytes. But I still can't run autodock3, same error message. I don't know how to get a stack size above 65536k. in the linux you can get unlimited stacksize for a process. Can anyone help me to get a stack size above 65536k in MAc OS X? Thank you in advance. jianquan chen Rutgers Univ. From chemistry-request@server.ccl.net Sat Oct 12 11:23:48 2002 Received: from rwcrmhc51.attbi.com ([204.127.198.38]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9CFNmB30743 for ; Sat, 12 Oct 2002 11:23:48 -0400 Received: from daveg-lifebook.cachesoftware.com ([12.224.252.81]) by rwcrmhc51.attbi.com (InterMail vM.4.01.03.27 201-229-121-127-20010626) with ESMTP id <20021012152342.UNYN4193.rwcrmhc51.attbi.com@daveg-lifebook.cachesoftware.com>; Sat, 12 Oct 2002 15:23:42 +0000 Message-Id: <5.1.0.14.0.20021012080732.0426d2a0@pop3.norton.antivirus> X-Sender: (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Sat, 12 Oct 2002 08:22:57 -0700 To: Connie Chang From: David Gallagher Subject: Re: CCL:Question about semi-empirical vs. tight-binding methods Cc: chemistry@ccl.net In-Reply-To: <3DA5A1B1.15AF8305@cornell.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi Connie, Cobalt parameters (and other transition metals) are now included for AM1, PM3 and PM5 in the latest version of MOPAC 2002 in CAChe 5.04. These have recently been developed by the author, J.J.P.Stewart. You can download a free evaluation version from http://www.cachesoftware.com/cache/cachedemo_win.shtml Also, you can input your own parameters into this version using the keyword "EXTERNAL=FILENAME". Regards David Gallagher, Fujitsu At 11:50 AM 10/10/2002 -0400, Connie Chang wrote: >Hi -- > >I'm trying to find the vibrational modes of a molecule (~100 atoms) >which has the elements carbon, nitrogen, oxygen, and cobalt in it. I've >tried doing this through commercial programs such as Hyperchem and >Gaussian, using the semi-empirical methods they provide (since the >ab-initio methods are too computer-intensive); but I'm not getting >sensible results. I suspect that part of the problem is because of the >presence of the cobalt. > >My advisor wants me to write my own code now with the logic that code we >write would be completely under our control as to what variables we >tweak... My question is which method would be the best to do this. > >Are semi-empirical methods the same as tight-binding methods? I know >that in tight binding methods, you use parameters for the Hamiltonian >matrix elements. And that you need to find the specific parameters for >the atom connectivity in your particular case. For example, since I >have a carbon bonded to a nitrogen for my molecule, I need to find >parameters specific to carbon-nitrogen connectivity. My question is is >there a way in either the semi-empirical or tight binding methods where >i would just need the parameters of the individual elements and there >would be some systematic way for me to get the parameters *between* >elements? > >Any suggestions, resources, etc. would be very helpful and appreciated. > >Thanks, >Connie Chang >cc236@cornell.edu > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net