From owner-chemistry@ccl.net Sat Jul 15 08:18:00 2006 From: "Richard Leo Wood rwoodphd#,#msn.com" To: CCL Subject: CCL: removing residues Message-Id: <-32141-060715081506-23728-DJo1GWZe79Xwe0xyo9VyTQ-$-server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Sat, 15 Jul 2006 08:15:00 -0400 Sent to CCL by: "Richard Leo Wood" [rwoodphd : msn.com] Hi all, I am currently working on analyzing a trajectory file from a series of MD calculations that I did. I'm slowly removing residues from the protein's active site (there are 13 residues), and then generating new trajectories. So far, I've removed one, two and three residues from the active site. My question to you is this: is there a way to figure out in advance how many possible unique combinations of a certain number of removed residues that I would have? In other words, how can I find out how many ways I can remove four residues (for example), or put another way, can I figure out how many trajectories will I have where I've removed unique combinations of four residues? Thank you, Richard From owner-chemistry@ccl.net Sat Jul 15 12:31:01 2006 From: "Wenrui Zheng wenruizheng:gmail.com" To: CCL Subject: CCL:G: Can we find the transition state of SN1 reaction by using Message-Id: <-32142-060714140829-15081-wB81pc24DuBRxegz3oKD+Q],[server.ccl.net> X-Original-From: "Wenrui Zheng" Date: Fri, 14 Jul 2006 14:08:29 -0400 Sent to CCL by: "Wenrui Zheng" [wenruizheng..gmail.com] Dear all, Recently I have failed to find the transition state of the first step of solvolyses of alkyl halide RX,for example tert-Butylchloride in methanol solvent by using Gaussian03. RX->R+ + X- Following the lengths of C-Cl increasing,the potential energy rises all along,which is the same with the case of in methanol solvent by using PCM model. Now I have some questions: 1. Can we on earth find the transition state of SN1 reaction by using Gaussian03? 2. Is traditional transition state theory adapt to any system for example this one ? If it is true then how can this kind of reaction happen and how can we calculate the reaction rate? Regards, Wenrui Zheng From owner-chemistry@ccl.net Sat Jul 15 13:05:00 2006 From: "Dominic Ryan dominic.ryan.:.comcast.net" To: CCL Subject: CCL: removing residues Message-Id: <-32143-060715122340-28881-UI6tqm9BNCzcdESD3ZqyzQ*o*server.ccl.net> X-Original-From: "Dominic Ryan" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sat, 15 Jul 2006 11:41:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Dominic Ryan" [dominic.ryan%x%comcast.net] The question really is, "what is a different trajectory"? When you are asking about how many different trajectories you will have you need to define what 'different' means to you. Are you looking for folding pathways? Enzyme regulatory motion (say a kinase loop)? Enzyme catalytic motion (say protease closing on substrate)? Is it differing time spent in a given state along a defined coordinate or is it following a motion path different by some minimal measure from the original path? Perhaps with that defined you could inspect the normal modes of the equilibrated full structure for clues as to the coupling with active site residues? Dominic -----Original Message----- > From: owner-chemistry(0)ccl.net [mailto:owner-chemistry(0)ccl.net] Sent: Saturday, July 15, 2006 7:45 AM To: Ryan, M Dominic Subject: CCL: removing residues Sent to CCL by: "Richard Leo Wood" [rwoodphd : msn.com] Hi all, I am currently working on analyzing a trajectory file from a series of MD calculations that I did. I'm slowly removing residues from the protein's active site (there are 13 residues), and then generating new trajectories. So far, I've removed one, two and three residues from the active site. My question to you is this: is there a way to figure out in advance how many possible unique combinations of a certain number of removed residues that I would have? In other words, how can I find out how many ways I can remove four residues (for example), or put another way, can I figure out how many trajectories will I have where I've removed unique combinations of four residues? Thank you, Richardhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Sat Jul 15 14:04:00 2006 From: "David F. Green dfgreen*o*ams.sunysb.edu" To: CCL Subject: CCL: removing residues Message-Id: <-32144-060715140158-19698-WAblihHHRp0J61iRYD+s6w#%#server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 15 Jul 2006 12:58:04 -0400 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen%a%ams.sunysb.edu] The binomial coefficient nCk gives the number of non-ordered sets of k elements from an initial sample of n. nCk = n! ------- (n-k)!k! ======================================================================= David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Math Tower, Room 1-117 Office: +1-631-632-9344 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================= Richard Leo Wood rwoodphd#,#msn.com wrote: > Sent to CCL by: "Richard Leo Wood" [rwoodphd : msn.com] > Hi all, > > I am currently working on analyzing a trajectory file from a series of MD calculations that I did. I'm slowly removing residues from the protein's active site (there are 13 residues), and then generating new trajectories. So far, I've removed one, two and three residues from the active site. > > My question to you is this: is there a way to figure out in advance how many possible unique combinations of a certain number of removed residues that I would have? In other words, how can I find out how many ways I can remove four residues (for example), or put another way, can I figure out how many trajectories will I have where I've removed unique combinations of four residues? > > Thank you, > Richard> > > From owner-chemistry@ccl.net Sat Jul 15 19:41:00 2006 From: "RICHARD JILL WOOD rwoodphd,+,msn.com" To: CCL Subject: CCL: removing residues Message-Id: <-32145-060715193757-32242-EO36vEtEnnJmKXqd0jRckg-*-server.ccl.net> X-Original-From: "RICHARD JILL WOOD" Content-Type: text/plain; format=flowed Date: Sat, 15 Jul 2006 22:25:22 +0000 Mime-Version: 1.0 Sent to CCL by: "RICHARD JILL WOOD" [rwoodphd^^^msn.com] Actually, I have 40 different trajectories of 40 MD simulations that I ran on a protein, 20 with a sugar bound, and 20 without. I removed the sugar and combined them into one large trajectory. I then wrote out a trajectory of just the active site residues, of which there are thirteen. My next goal was to find which residues are important in the binding of the sugar and which aren't. I have been using PCA to do this. With all the residues I get two "blobs". My goal is to see if I can get one of these "blobs" to disappear by selectively removing a residue (or two, or three, ... etc.), save these as a new trajectory, and then do PCA. I am now up to removing four residues, which means I have nine active sites left in my trajectories. I have been writing them out on a piece of paper and I wanted to know if there was a way that I could compute how many of these files I should have for a given number of residues removed, that way I could check that I was being thorough. I hope this clears things up. >From: "Dominic Ryan dominic.ryan.:.comcast.net" >Reply-To: "CCL Subscribers" >To: "Wood, Richard L. " >Subject: CCL: removing residues >Date: Sat, 15 Jul 2006 15:09:58 -0400 > >Sent to CCL by: "Dominic Ryan" [dominic.ryan%x%comcast.net] >The question really is, "what is a different trajectory"? When you are >asking about how many different trajectories you will have you need to >define what 'different' means to you. > >Are you looking for folding pathways? Enzyme regulatory motion (say a >kinase loop)? Enzyme catalytic motion (say protease closing on substrate)? >Is it differing time spent in a given state along a defined coordinate or >is >it following a motion path different by some minimal measure from the >original path? > >Perhaps with that defined you could inspect the normal modes of the >equilibrated full structure for clues as to the coupling with active site >residues? > >Dominic > > >-----Original Message----- > > From: owner-chemistry---ccl.net [mailto:owner-chemistry---ccl.net] >Sent: Saturday, July 15, 2006 7:45 AM >To: Ryan, M Dominic >Subject: CCL: removing residues > >Sent to CCL by: "Richard Leo Wood" [rwoodphd : msn.com] >Hi all, > >I am currently working on analyzing a trajectory file from a series of MD >calculations that I did. I'm slowly removing residues from the protein's >active site (there are 13 residues), and then generating new trajectories. >So far, I've removed one, two and three residues from the active site. > >My question to you is this: is there a way to figure out in advance how >many >possible unique combinations of a certain number of removed residues that I >would have? In other words, how can I find out how many ways I can remove >four residues (for example), or put another way, can I figure out how many >trajectories will I have where I've removed unique combinations of four >residues? > >Thank you, >Richardhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt> > > _________________________________________________________________ Is your PC infected? Get a FREE online computer virus scan from McAfeeŽ Security. http://clinic.mcafee.com/clinic/ibuy/campaign.asp?cid=3963