From owner-chemistry@ccl.net Sun Jul 16 08:40:01 2006 From: "John McKelvey jmmckel|a|attglobal.net" To: CCL Subject: CCL:G: Can we find the transition state of SN1 reaction by using Message-Id: <-32146-060715155607-12013-JreSi3nAslcdyDEdyKto3A _ server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 15 Jul 2006 15:46:09 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel^^attglobal.net] What about adding one molecule of methanol in a configuration to H-bond with the Cl(-) with a second molecule with the O-lp's approaching the tertiary carbon from the rear, all in the PVM model? My $0.02 John McKelvey Wenrui Zheng wenruizheng:gmail.com wrote: >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 Sun Jul 16 10:39:00 2006 From: "Steve Bowlus chezbowlus_._goldrush.com" To: CCL Subject: CCL:G: Can we find the transition state of SN1 reaction by using Message-Id: <-32147-060715194707-510-zOwLTmhGM9k2N/kC23QQCg^^server.ccl.net> X-Original-From: Steve Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 15 Jul 2006 15:48:15 -0700 MIME-Version: 1.0 Sent to CCL by: Steve Bowlus [chezbowlus!A!goldrush.com] It would not surprise me that this type of reaction must be modeled with explicit solvent. Stabilization of the products relative to the TS is attained by solvation of the separated ions, i.e. the physical "flow" of solvent between the nascent ions, and the direct (dipolar?) interaction of solvent with the ions. Most physical organic books should have a discussion of solvent-separated reaction partners, and most likely SN1 reactions in particular. Cheers, Steve Wenrui Zheng wenruizheng:gmail.com wrote: > 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 Sun Jul 16 11:13:00 2006 From: "hossameldin elgabarty h_elgabarty%%hotmail.com" To: CCL Subject: CCL: Nucleophilic Susceptibility Message-Id: <-32148-060716075107-13788-oaV2861i2qMW6mcsnstxAg()server.ccl.net> X-Original-From: "hossameldin elgabarty" Content-Type: text/plain; format=flowed Date: Sun, 16 Jul 2006 12:43:12 +0300 Mime-Version: 1.0 Sent to CCL by: "hossameldin elgabarty" [h_elgabarty/a\hotmail.com] Dear All, I am trying to calculate the nucleophilic susceptibility (as a descriptor in a QSAR analysis) using a PM3 wavefunction, however,I only found the formula for HMO theory. Can any one help? should i just use the same formula as in HMO, taking the sum over all the basis functions? Thanks _________________________________________________________________ Express yourself instantly with MSN Messenger! Download today it's FREE! http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/ From owner-chemistry@ccl.net Sun Jul 16 15:44:00 2006 From: "MIQUEL =?iso-8859-1?Q?SOL=C0_I_PUIG?= miquel.sola]_[udg.es" To: CCL Subject: CCL:G: Can we find the transition state of SN1 reaction by using Message-Id: <-32149-060716143737-11644-GfsV69P2lpZpHQvNc3AtUg**server.ccl.net> X-Original-From: MIQUEL =?iso-8859-1?Q?SOL=C0_I_PUIG?= Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Sun, 16 Jul 2006 18:28:00 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: MIQUEL =?iso-8859-1?Q?SOL=C0_I_PUIG?= [miquel.sola.^.udg.es] Dear Wenrui and Steve, We addressed this question some years ago. We found that the energy profile for the Ch3Cl -> CH3+ + Cl- reaction in the gas phase increases monotonically, whereas the presence of either uniform electric fields or solvents changes the energy profile, causing the appearance of a transition state and the increase of the exothermicity of the process. The reference is: M. Solŕ, E. Carbonell, A. Lledós, M. Duran and J. Bertrán. "Ab initio study of the effect of external perturbations in the dissociation of CH3Cl" J. Mol. Struct. (THEOCHEM) 255 (1992) 283-296. Hope this helps, Miquel > Sent to CCL by: Steve Bowlus [chezbowlus!A!goldrush.com] > It would not surprise me that this type of reaction must be modeled with > explicit solvent. Stabilization of the products relative to the TS is > attained by solvation of the separated ions, i.e. the physical "flow" of > solvent between the nascent ions, and the direct (dipolar?) interaction > of solvent with the ions. Most physical organic books should have a > discussion of solvent-separated reaction partners, and most likely SN1 > reactions in particular. > > Cheers, > Steve > > > Wenrui Zheng wenruizheng:gmail.com wrote: >> 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 Sun Jul 16 19:43:00 2006 From: "Neeraj Misra misraneeraj~~gmail.com" To: CCL Subject: CCL: gaussian calculations Message-Id: <-32150-060716194220-22389-0aIcy8BCDjCpfpE0JeUA6A]_[server.ccl.net> X-Original-From: "Neeraj Misra" Date: Sun, 16 Jul 2006 19:42:18 -0400 Sent to CCL by: "Neeraj Misra" [misraneeraj-*-gmail.com] HOW CAN WE PERFORM AB INITIO CALCULATIONS (AND WHAT TYPE) ON A CHEMICAL REACTION.WHAT ARE THE POSSIBILITIES OF CALCULATIONS AND IMPORTANCE TOO. ANY HELP WOULD BE GREATLY ACKNOWLEDGED. THANKS IN ADVANCE From owner-chemistry@ccl.net Sun Jul 16 23:34:01 2006 From: "dstrahs() pace.edu" To: CCL Subject: CCL: removing residues Message-Id: <-32151-060715235345-31667-uFk3d5/DKPc6uy8VrtaSqQ.@.server.ccl.net> X-Original-From: dstrahs ~ pace.edu Content-language: en Content-type: multipart/alternative; boundary="Boundary_(ID_2Ec1rwOgiUWPtz6cZ0643g)" Date: Sun, 16 Jul 2006 03:12:06 +0000 (GMT) MIME-version: 1.0 Sent to CCL by: dstrahs::pace.edu This is a multi-part message in MIME format. --Boundary_(ID_2Ec1rwOgiUWPtz6cZ0643g) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: quoted-printable Content-disposition: inline Richard=3A I think you=27re asking about the number of combinations of 9 elements y= ou can have from 13 elements total=2E This is the binomial expansion=3A =23 combinations =3D nCr =3D n! / =5B= (n-r)! r!=5D For your example=2C n=3D13 and r =3D 9 (or r =3D 4=3B it gives the same = answer either way)=2E Thus=2C =23 combinations =3D 13 ! / =5B9! 4!=5D =3D 715=2E Dan Strahs ----- Original Message ----- > From=3A =22RICHARD JILL WOOD rwoodphd=2C+=2Cmsn=2Ecom=22 = Date=3A Saturday=2C July 15=2C 2006 10=3A59 pm Subject=3A CCL=3A removing residues To=3A =22Strahs=2C Daniel -id=233jy-=22 = =3E Sent to CCL by=3A =22RICHARD JILL WOOD=22 =5Brwoodphd=5E=5E=5Emsn=2E= com=5D =3E = =3E Actually=2C I have 40 different trajectories of 40 MD simulations = =3E that I ran = =3E on a protein=2C 20 with a sugar bound=2C and 20 without=2E I removed= = =3E the sugar = =3E and combined them into one large trajectory=2E =3E = =3E I then wrote out a trajectory of just the active site residues=2C = =3E of which = =3E there are thirteen=2E My next goal was to find which residues are = =3E important = =3E in the binding of the sugar and which aren=27t=2E =3E = =3E I have been using PCA to do this=2E With all the residues I get = =3E two =22blobs=22=2E = =3E My goal is to see if I can get one of these =22blobs=22 to disappear= = =3E by = =3E selectively removing a residue (or two=2C or three=2C =2E=2E=2E etc=2E= )=2C = =3E save these as a = =3E new trajectory=2C and then do PCA=2E I am now up to removing four = =3E residues=2C = =3E which means I have nine active sites left in my trajectories=2E I = =3E have been = =3E writing them out on a piece of paper and I wanted to know if = =3E there was a way = =3E that I could compute how many of these files I should have for a = =3E given = =3E number of residues removed=2C that way I could check that I was = =3E being = =3E thorough=2E =3E = =3E I hope this clears things up=2E =3E = =3E =3EFrom=3A =22Dominic Ryan dominic=2Eryan=2E=3A=2Ecomcast=2Enet=22 =3E= chemistry=5Eccl=2Enet=3E=3EReply-To=3A =22CCL Subscribers=22 = =3E =3ETo=3A =22Wood=2C Richard L=2E =22 = =3E =3ESubject=3A CCL=3A removing residues =3E =3EDate=3A Sat=2C 15 Jul 2006 15=3A09=3A58 -0400 =3E =3E =3E =3ESent to CCL by=3A =22Dominic Ryan=22 =5Bdominic=2Eryan=25x=25comc= ast=2Enet=5D =3E =3EThe question really is=2C =22what is a different trajectory=22=3F= When = =3E you are =3E =3Easking about how many different trajectories you will have you = =3E need to =3E =3Edefine what =27different=27 means to you=2E =3E =3E =3E =3EAre you looking for folding pathways=3F Enzyme regulatory motion = =3E (say a =3E =3Ekinase loop)=3F Enzyme catalytic motion (say protease closing on = =3E substrate)=3F=3EIs it differing time spent in a given state along a = =3E defined coordinate or = =3E =3Eis =3E =3Eit following a motion path different by some minimal measure = =3E from the =3E =3Eoriginal path=3F =3E =3E =3E =3EPerhaps with that defined you could inspect the normal modes of t= he =3E =3Eequilibrated full structure for clues as to the coupling with = =3E active site =3E =3Eresidues=3F =3E =3E =3E =3EDominic =3E =3E =3E =3E =3E =3E-----Original Message----- =3E =3E =3E From=3A owner-chemistry---ccl=2Enet =5Bmailto=3Aowner-chemis= try---ccl=2Enet=5D =3E =3ESent=3A Saturday=2C July 15=2C 2006 7=3A45 AM =3E =3ETo=3A Ryan=2C M Dominic =3E =3ESubject=3A CCL=3A removing residues =3E =3E =3E =3ESent to CCL by=3A =22Richard Leo Wood=22 =5Brwoodphd =3A msn=2Eco= m=5D =3E =3EHi all=2C =3E =3E =3E =3EI am currently working on analyzing a trajectory file from a = =3E series of MD =3E =3Ecalculations that I did=2E I=27m slowly removing residues from th= e = =3E protein=27s=3Eactive site (there are 13 residues)=2C and then = =3E generating new trajectories=2E =3E =3ESo far=2C I=27ve removed one=2C two and three residues from the = =3E active site=2E =3E =3E =3E =3EMy question to you is this=3A is there a way to figure out in = =3E advance how = =3E =3Emany =3E =3Epossible unique combinations of a certain number of removed = =3E residues that I =3E =3Ewould have=3F In other words=2C how can I find out how many ways = I = =3E can remove =3E =3Efour residues (for example)=2C or put another way=2C can I figure= = =3E out how many =3E =3Etrajectories will I have where I=27ve removed unique combinations= = =3E of four =3E =3Eresidues=3F =3E =3E =3E =3EThank you=2C =3E =3ERichardhttp=3A//www=2Eccl=2Enet/cgi- =3E bin/ccl/send=5Fccl=5Fmessagehttp=3A//www=2Eccl=2Enet/chemistry/sub=5F= unsub=2Eshtmlhttp=3A//www=2Eccl=2Enet/spammers=2Etxt=3E=3E =3E =3E =3E = =3E =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F =3E Is your PC infected=3F Get a FREE online computer virus scan from = =3E McAfee=AE = =3E Security=2E http=3A//clinic=2Emcafee=2Ecom/clinic/ibuy/campaign=2Eas= p=3Fcid=3D3963 =3E = =3E = =3E = =3E -=3D This is automatically added to each message by the mailing = =3E script =3D- =3E To recover the email address of the author of the message=2C = =3E please change =3E the strange characters on the top line to the =40 sign=2E You can al= so =3E look up the X-Original-From=3A line in the mail header=2E =3E = =3E E-mail to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or use =3E http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage =3E = =3E Subscribe/Unsubscribe=3A = =3E http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml =3E = =3E Before posting=2C check wait time at=3A http=3A//www=2Eccl=2Enet =3E = =3E Job=3A http=3A//www=2Eccl=2Enet/jobs = =3E Conferences=3A = =3E http=3A//server=2Eccl=2Enet/chemistry/announcements/conferences/ =3E Search Messages=3A http=3A//www=2Eccl=2Enet/htdig (login=3A ccl=2C = =3E Password=3A search) =3E = =3E If your mail bounces from CCL with 5=2E7=2E1 error=2C check=3A =3E http=3A//www=2Eccl=2Enet/spammers=2Etxt =3E = =3E RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/ =3E = =3E -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- =3E +-+-+-+ =3E = =3E = =3E = =3E --Boundary_(ID_2Ec1rwOgiUWPtz6cZ0643g) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: quoted-printable Content-disposition: inline =3CDIV=3ERichard=3A=3C/DIV=3E =3CDIV=3E=26nbsp=3B=3C/DIV=3E =3CDIV=3EI think you=27re asking about the number of combinations of 9 e= lements you can have=26nbsp=3Bfrom 13 elements total=2E=3C/DIV=3E =3CDIV=3E=26nbsp=3B=3C/DIV=3E =3CDIV=3EThis is the binomial expansion=3A =23 combinations=26nbsp=3B=3D= =26nbsp=3BnCr=26nbsp=3B=3D=26nbsp=3B n! / =5B(n-r)! r!=5D=3C/DIV=3E =3CDIV=3EFor=26nbsp=3Byour example=2C n=3D13 and r =3D 9 (or r =3D 4=3B = it gives the same answer either way)=2E=3C/DIV=3E =3CDIV=3EThus=2C =23 combinations =3D 13 ! / =5B9! 4!=5D =3D 715=2E=3C/D= IV=3E =3CDIV=3E=26nbsp=3B=3C/DIV=3E =3CDIV=3EDan Strahs=3C/DIV=3E =3CDIV=3E=26nbsp=3B=3C/DIV=3E =3CDIV=3E=3CBR=3E----- Original Message -----=3CBR=3EFrom=3A =22RICHARD = JILL WOOD rwoodphd=2C+=2Cmsn=2Ecom=22 =3COWNER-CHEMISTRY=40CCL=2ENET=3E=3C= BR=3EDate=3A Saturday=2C July 15=2C 2006 10=3A59 pm=3CBR=3ESubject=3A CC= L=3A removing residues=3CBR=3ETo=3A =22Strahs=2C Daniel -id=233jy-=22 =3C= DSTRAHS=40PACE=2EEDU=3E=3CBR=3E=3CBR=3E=26gt=3B Sent to CCL by=3A =22RIC= HARD JILL WOOD=22 =5Brwoodphd=5E=5E=5Emsn=2Ecom=5D=3CBR=3E=26gt=3B =3CBR= =3E=26gt=3B Actually=2C I have 40 different trajectories of 40 MD simula= tions =3CBR=3E=26gt=3B that I ran =3CBR=3E=26gt=3B on a protein=2C 20 wi= th a sugar bound=2C and 20 without=2E I removed =3CBR=3E=26gt=3B the sug= ar =3CBR=3E=26gt=3B and combined them into one large trajectory=2E=3CBR=3E= =26gt=3B =3CBR=3E=26gt=3B I then wrote out a trajectory of just the acti= ve site residues=2C =3CBR=3E=26gt=3B of which =3CBR=3E=26gt=3B there are= thirteen=2E My next goal was to find which residues are =3CBR=3E=26gt=3B= important =3CBR=3E=26gt=3B in the binding of the sugar and which aren=27= t=2E=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B I have been using PCA to do this=2E= With all the residues I get =3CBR=3E=26gt=3B two =22blobs=22=2E =3CBR=3E= =26gt=3B My goal is to see if I can get one of these =22blobs=22 to disa= ppear =3CBR=3E=26gt=3B by =3CBR=3E=26gt=3B selectively removing a residu= e (or two=2C or three=2C =2E=2E=2E etc=2E)=2C =3CBR=3E=26gt=3B save thes= e as a =3CBR=3E=26gt=3B new trajectory=2C and then do PCA=2E I am now up= to removing four =3CBR=3E=26gt=3B residues=2C =3CBR=3E=26gt=3B which me= ans I have nine active sites left in my trajectories=2E I =3CBR=3E=26gt=3B= have been =3CBR=3E=26gt=3B writing them out on a piece of paper and I w= anted to know if =3CBR=3E=26gt=3B there was a way =3CBR=3E=26gt=3B that = I could compute how many of these files I should have for a =3CBR=3E=26g= t=3B given =3CBR=3E=26gt=3B number of residues removed=2C that way I cou= ld check that I was =3CBR=3E=26gt=3B being =3CBR=3E=26gt=3B thorough=2E=3C= BR=3E=26gt=3B =3CBR=3E=26gt=3B I hope this clears things up=2E=3CBR=3E=26= gt=3B =3CBR=3E=26gt=3B =26gt=3BFrom=3A =22Dominic Ryan dominic=2Eryan=2E= =3A=2Ecomcast=2Enet=22 =3COWNER-=3CBR=3E=26gt=3B chemistry=5Eccl=2Enet=26= gt=3B=26gt=3BReply-To=3A =22CCL Subscribers=22 =3CCHEMISTRY=5ECCL=2ENET=3E= =3CBR=3E=26gt=3B =26gt=3BTo=3A =22Wood=2C Richard L=2E =22 =3CRWOODPHD=5E= MSN=2ECOM=3E=3CBR=3E=26gt=3B =26gt=3BSubject=3A CCL=3A removing residues= =3CBR=3E=26gt=3B =26gt=3BDate=3A Sat=2C 15 Jul 2006 15=3A09=3A58 -0400=3C= BR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BSent to CCL by=3A =22Domi= nic Ryan=22 =5Bdominic=2Eryan=25x=25comcast=2Enet=5D=3CBR=3E=26gt=3B =26= gt=3BThe question really is=2C =22what is a different trajectory=22=3F W= hen =3CBR=3E=26gt=3B you are=3CBR=3E=26gt=3B =26gt=3Basking about how ma= ny different trajectories you will have you =3CBR=3E=26gt=3B need to=3CB= R=3E=26gt=3B =26gt=3Bdefine what =27different=27 means to you=2E=3CBR=3E= =26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BAre you looking for folding pa= thways=3F Enzyme regulatory motion =3CBR=3E=26gt=3B (say a=3CBR=3E=26gt=3B= =26gt=3Bkinase loop)=3F Enzyme catalytic motion (say protease closing o= n =3CBR=3E=26gt=3B substrate)=3F=26gt=3BIs it differing time spent in a = given state along a =3CBR=3E=26gt=3B defined coordinate or =3CBR=3E=26gt= =3B =26gt=3Bis=3CBR=3E=26gt=3B =26gt=3Bit following a motion path differ= ent by some minimal measure =3CBR=3E=26gt=3B from the=3CBR=3E=26gt=3B =26= gt=3Boriginal path=3F=3CBR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BP= erhaps with that defined you could inspect the normal modes of the=3CBR=3E= =26gt=3B =26gt=3Bequilibrated full structure for clues as to the couplin= g with =3CBR=3E=26gt=3B active site=3CBR=3E=26gt=3B =26gt=3Bresidues=3F=3C= BR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BDominic=3CBR=3E=26gt=3B =26= gt=3B=3CBR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3B-----Original Mes= sage-----=3CBR=3E=26gt=3B =26gt=3B =26gt=3B From=3A owner-chemistry---cc= l=2Enet =5Bmailto=3Aowner-chemistry---ccl=2Enet=5D=3CBR=3E=26gt=3B =26gt= =3BSent=3A Saturday=2C July 15=2C 2006 7=3A45 AM=3CBR=3E=26gt=3B =26gt=3B= To=3A Ryan=2C M Dominic=3CBR=3E=26gt=3B =26gt=3BSubject=3A CCL=3A removi= ng residues=3CBR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BSent to CCL= by=3A =22Richard Leo Wood=22 =5Brwoodphd =3A msn=2Ecom=5D=3CBR=3E=26gt=3B= =26gt=3BHi all=2C=3CBR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BI am= currently working on analyzing a trajectory file from a =3CBR=3E=26gt=3B= series of MD=3CBR=3E=26gt=3B =26gt=3Bcalculations that I did=2E I=27m s= lowly removing residues from the =3CBR=3E=26gt=3B protein=27s=26gt=3Bact= ive site (there are 13 residues)=2C and then =3CBR=3E=26gt=3B generating= new trajectories=2E=3CBR=3E=26gt=3B =26gt=3BSo far=2C I=27ve removed on= e=2C two and three residues from the =3CBR=3E=26gt=3B active site=2E=3CB= R=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BMy question to you is this= =3A is there a way to figure out in =3CBR=3E=26gt=3B advance how =3CBR=3E= =26gt=3B =26gt=3Bmany=3CBR=3E=26gt=3B =26gt=3Bpossible unique combinatio= ns of a certain number of removed =3CBR=3E=26gt=3B residues that I=3CBR=3E= =26gt=3B =26gt=3Bwould have=3F In other words=2C how can I find out how = many ways I =3CBR=3E=26gt=3B can remove=3CBR=3E=26gt=3B =26gt=3Bfour res= idues (for example)=2C or put another way=2C can I figure =3CBR=3E=26gt=3B= out how many=3CBR=3E=26gt=3B =26gt=3Btrajectories will I have where I=27= ve removed unique combinations =3CBR=3E=26gt=3B of four=3CBR=3E=26gt=3B = =26gt=3Bresidues=3F=3CBR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =26gt=3BTha= nk you=2C=3CBR=3E=26gt=3B =26gt=3BRichardhttp=3A//www=2Eccl=2Enet/cgi-=3C= BR=3E=26gt=3B bin/ccl/send=5Fccl=5Fmessagehttp=3A//www=2Eccl=2Enet/chemi= stry/sub=5Funsub=2Eshtmlhttp=3A//www=2Eccl=2Enet/spammers=2Etxt=26gt=3B=26= gt=3B=3CBR=3E=26gt=3B =26gt=3B=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B =5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F= =5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=5F=3CBR=3E=26gt=3B Is your PC in= fected=3F Get a FREE online computer virus scan from =3CBR=3E=26gt=3B Mc= Afee=AE =3CBR=3E=26gt=3B Security=2E http=3A//clinic=2Emcafee=2Ecom/clin= ic/ibuy/campaign=2Easp=3Fcid=3D3963=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B =3C= BR=3E=26gt=3B =3CBR=3E=26gt=3B -=3D This is automatically added to each = message by the mailing =3CBR=3E=26gt=3B script =3D-=3CBR=3E=26gt=3B To r= ecover the email address of the author of the message=2C =3CBR=3E=26gt=3B= please change=3CBR=3E=26gt=3B the strange characters on the top line to= the =40 sign=2E You can also=3CBR=3E=26gt=3B look up the X-Original-Fro= m=3A line in the mail header=2E=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B E-mail = to subscribers=3A CHEMISTRY=40ccl=2Enet or use=3A=3CBR=3E=26gt=3B http=3A= //www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fmessage=3CBR=3E=26gt=3B =3CBR= =3E=26gt=3B E-mail to administrators=3A CHEMISTRY-REQUEST=40ccl=2Enet or= use=3CBR=3E=26gt=3B http=3A//www=2Eccl=2Enet/cgi-bin/ccl/send=5Fccl=5Fm= essage=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Subscribe/Unsubscribe=3A =3CBR=3E= =26gt=3B http=3A//www=2Eccl=2Enet/chemistry/sub=5Funsub=2Eshtml=3CBR=3E=26= gt=3B =3CBR=3E=26gt=3B Before posting=2C check wait time at=3A http=3A//= www=2Eccl=2Enet=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B Job=3A http=3A//www=2Ec= cl=2Enet/jobs =3CBR=3E=26gt=3B Conferences=3A =3CBR=3E=26gt=3B http=3A//= server=2Eccl=2Enet/chemistry/announcements/conferences/=3CBR=3E=26gt=3B = Search Messages=3A http=3A//www=2Eccl=2Enet/htdig (login=3A ccl=2C =3CBR= =3E=26gt=3B Password=3A search)=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B If your= mail bounces from CCL with 5=2E7=2E1 error=2C check=3A=3CBR=3E=26gt=3B = http=3A//www=2Eccl=2Enet/spammers=2Etxt=3CBR=3E=26gt=3B =3CBR=3E=26gt=3B= RTFI=3A http=3A//www=2Eccl=2Enet/chemistry/aboutccl/instructions/=3CBR=3E= =26gt=3B =3CBR=3E=26gt=3B -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+= -+-+-+-+-+-+-+-+-+-=3CBR=3E=26gt=3B +-+-+-+=3CBR=3E=26gt=3B =3CBR=3E=26g= t=3B =3CBR=3E=26gt=3B =3CBR=3E=26gt=3B =3C/DIV=3E --Boundary_(ID_2Ec1rwOgiUWPtz6cZ0643g)--