From owner-chemistry@ccl.net Sun Nov 9 01:14:01 2008 From: "Scott Dixon scott[A]daylight.com" To: CCL Subject: CCL:G: Two not-so-related questions Message-Id: <-38065-081109011145-18356-9zUnCXGfQDLavvFBqBypyA^server.ccl.net> X-Original-From: Scott Dixon Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sat, 8 Nov 2008 22:11:32 -0800 Mime-Version: 1.0 (Apple Message framework v929.2) Sent to CCL by: Scott Dixon [scott/a\daylight.com] Hi, Joe- On Nov 8, 2008, at 12:23 PM, 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. > > 2. Has there been work on creating visualizations of "conformer > envelopes", graphical representations of the conformational space > occupied (or available) to molecules. Particularly when such > visualizations are used to (quickly/visually) compare whether 2 > molecules can adopt the same shape - or if there are shapes of one > that can't be adopted by another. Interestingly, this goes back to some of the early computational chemistry/computer graphics work by Garland Marshall and his group. They called it the active analog approach and it was first described at an ACS meeting in 1979. They computed available conformations and used gaussians to compute composite volumes for actives and inactives and compared them to see if the inactives required extra volume compared to the actives. They contoured the volumes for graphics display. You can read about the history of this work in Garland's chapter in the book "Chemoinformatics in Drug Discovery" edited by Tudor Oprea. Cheers, Scott From owner-chemistry@ccl.net Sun Nov 9 15:09:01 2008 From: "Marcus Vinicius Batista genetics.marcus,gmail.com" To: CCL Subject: CCL: Problems with NAMD simulations Message-Id: <-38066-081109145546-8386-sd3I4UxXtGTQDBdiwicT9w-.-server.ccl.net> X-Original-From: "Marcus Vinicius Batista" Date: Sun, 9 Nov 2008 14:55:41 -0500 Sent to CCL by: "Marcus Vinicius Batista" [genetics.marcus..gmail.com] 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.