From owner-chemistry@ccl.net Mon Mar 29 08:41:44 2010 From: "Jan Labanowski janl(a)speakeasy.net" To: CCL Subject: CCL: CCL is not fully operational yet Message-Id: <-41535-100329015712-8427-l5pZr5/qGKN338Bfu0tk5Q::server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 29 Mar 2010 00:57:03 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl,,speakeasy.net] Dear CCL, As some of you noticted, the CCL is not fully operational yet. On Friday, before 3am or so, the CCL disk has been shreaded to pieces. The problem is that my HD LED on the server is constantly red. There are often = 30-40 thousands/day attempts of spamming CCL, about 10k attempts to crack my pass= words, thousands of attempts to place porn in the ftp incoming directory, and so o= n... On top of it, there is also some legitimate traffic from users and search engines. If you think that RAID would help, believe me, it would not. Only = the complete backup server would work, but the synchronization is always a prob= lem since you do not want to do it automatically, unless you capture the system= image every some minutes. But I do not have SAN in my basement and do not run clu= sters, so this is not a feasible solution. However, I will create a backup server = (I actually configure both: primary and secondary in parallel as I go through = this exercise). Instead of just putting new disks, restoring content from backups and reboo= ting CCL, I decided to upgrade and optimize the CCL and rearrange things to diff= erent partitions by doing links to spread the load and have an option to backup o= ften changing content frequently. This of course is not liked by Selinux and sen= dmail so I have to do a lot of reconfiguration. Moreover, I updated all packages = to the latest gratest from Fedora 12, and they of course now use different user_id= s, group_ids and have config files that are not backward compatible. And this = takes time... I also decided to put CCL on a new server that is roughly 3 times m= ore powerful. So bear with me... The home page http://www.ccl.net will have the status. While I did not leave my basement over the weekend, I will have les= s time over the week.=20 Jan From owner-chemistry@ccl.net Mon Mar 29 23:55:00 2010 From: "V ctor Alejandro Gil Sep lveda victor.gil.sepulveda#,#gmail.com" To: CCL Subject: CCL: Tinker .prm (force field parameters) file specs Message-Id: <-41536-100329074923-17489-WoMYcoEwn/qIriXhAHGkhg~!~server.ccl.net> X-Original-From: "V ctor Alejandro Gil Sep lveda" Date: Mon, 29 Mar 2010 07:49:22 -0400 Sent to CCL by: "V ctor Alejandro Gil Sep lveda" [victor.gil.sepulveda|*|gmail.com] Dear all, We are trying to use the tinker .prm force field parameter files for our minimization software as a standard. The file format seems to be very straightforward , however we don't want to do wrong assumptions. After googling I haven't found the specs anywhere, anyone knows where can I find them? (with specs I mean, type of the atom from char1 to char 6, identifier from char 8 to 10 and so on...) Thanks to all!! Vctor