From owner-chemistry@ccl.net Wed Apr 15 10:42:01 2015 From: "Peter Kraus p.kraus12() imperial.ac.uk" To: CCL Subject: CCL:G: Calculating Variational TS Message-Id: <-51258-150415103929-11093-NWNTFH34voZ5sO6eL7LqHA-#-server.ccl.net> X-Original-From: "Peter Kraus" Date: Wed, 15 Apr 2015 10:39:27 -0400 Sent to CCL by: "Peter Kraus" [p.kraus12{:}imperial.ac.uk] Dear CCL Subscribers, I am looking for a way to estimate/calculate a "variational transition state" for an essentially barrierless association process. Currently, I have Gaussian opt-freq logfiles of the reactants and of the product, and a logfile of an "intermediate" somewhere on the minimum energy path from products to the reactants. I was told there is a program which can take these three structures as input, and perform some sort of variational optimisation without a considerable computational expense, unfortunately I don't know the name of the code. The only code related to VTST I could find was POLYRATE (in its RP-VTST nosaddle mode); I'm not sure whether this is the right tool. I'll be glad for any help and pointers. Thanks in advance, Peter Kraus From owner-chemistry@ccl.net Wed Apr 15 20:50:01 2015 From: "Ben R Fritch brf141*psu.edu" To: CCL Subject: CCL: Parameters for covalent bond between serine and adenine Message-Id: <-51259-150415202428-12629-PduVcCZ/NsNSvUoNrO3ndA(!)server.ccl.net> X-Original-From: "Ben R Fritch" Date: Wed, 15 Apr 2015 20:24:26 -0400 Sent to CCL by: "Ben R Fritch" [brf141 ~~ psu.edu] Hi, I have a patch that covalently bonds the CCA end of tRNA (ON2 of adenine) to a protein residue (carbonyl carbon). The parameterization of this patch is very important. Does anybody know of a forcefield parameter file that contains the parameters for this covalent bond (bond, charge, angle, dihedral, etc.)? Has anybody parameterized a patch for this bond or know of where I can find these parameters in the literature? Thank you for your time.