From owner-chemistry@ccl.net Thu Aug 3 10:49:00 2006 From: "Keith Tobias Butler keeeto2000##yahoo.co.uk" To: CCL Subject: CCL:G: RM1 Implimentation In gaussian 03 Message-Id: <-32333-060803104724-32181-ui+blySKpQ3Q1biC0HaDcQ|a|server.ccl.net> X-Original-From: "Keith Tobias Butler" Date: Thu, 3 Aug 2006 10:47:24 -0400 Sent to CCL by: "Keith Tobias Butler" [keeeto2000- -yahoo.co.uk] Dear Members, I have succesfully implimented RM1 in Gaussian 03. It is simply a matter of modifying the utilam.F file, however some values which are derived from the parameters in MOPAC are included as data in Gaussian, so you will need to change these values also. They are not included in the original paper, if anybody is interested I have a spreadsheet, which unfortunatly I cannot attach to this email, containing all necessary parameters. Also Dr.Simas who's address is on the original paper has this spreadsheet. I have tested RM1 and preliminary results are promising, it shows significant improvement over AM1 values compared to DFT, particularly for pi-systems containing N atoms, eg a pyridinium system. Keith T. Butler. From owner-chemistry@ccl.net Thu Aug 3 11:24:01 2006 From: "Bala subramanian bala(!)igib.res.in" To: CCL Subject: CCL: generating RNA structures Message-Id: <-32334-060802231403-7574-g/hHM0zXYbU0/cDjQSbwcA:server.ccl.net> X-Original-From: "Bala subramanian" Date: Wed, 2 Aug 2006 23:14:03 -0400 Sent to CCL by: "Bala subramanian" [bala]![igib.res.in] Dear cclers, Is there any free software using which i can create unusal RNA structures. I have to construct a structure which has some bulge part in one strand. I tried with insightII but it can generate only standard duplex forms. Also in my RNA there are some mismatches which i couldnt generate with insightII. thank you, Balasubramanian IGIB, Delhi From owner-chemistry@ccl.net Thu Aug 3 11:59:00 2006 From: "Charlie Chand chucks.mail*gmail.com" To: CCL Subject: CCL: Autodock Docking: Docking with NADP Message-Id: <-32335-060803033853-25045-6luLcmXK8k2VadO2OsR0oQ : server.ccl.net> X-Original-From: "Charlie Chand" Date: Thu, 3 Aug 2006 03:38:52 -0400 Sent to CCL by: "Charlie Chand" [chucks.mail|*|gmail.com] Dear CCL Users, Hello. I am interested in docking a ligand into a receptor with NADP using Autodock version 305 with ADT version 1.4.1. When doing Autogrid I discover the following type error. Is Autodock robust enough to account for the phosphates or is there a special procedure to account for the phosphates? /home/comp/Desktop/dist305/bin/i86Linux2/autogrid3: WARNING! Atom type error, c an't find type for "P1 " in typelist "CNOSHXM". /home/comp/Desktop/dist305/bin/i86Linux2/autogrid3: WARNING! Atom type error, c an't find type for "P " in typelist "CNOSHXM". /home/comp/Desktop/dist305/bin/i86Linux2/autogrid3: WARNING! Atom type error, c an't find type for "P2 " in typelist "CNOSHXM". /home/comp/Desktop/dist305/bin/i86Linux2/autogrid3: WARNING! Atom type error, c an't find type for "P1 " in typelist "CNOSHXM". /home/comp/Desktop/dist305/bin/i86Linux2/autogrid3: WARNING! Atom type error, c an't find type for "P2 " in typelist "CNOSHXM". /home/comp/Desktop/dist305/bin/i86Linux2/autogrid3: WARNING! Atom type error, c an't find type for "P3 " in typelist "CNOSHXM". I can skip through these errors and follow through to Autodock which runs and outputs a result. I found this chart on the Autodock Dock site: nbp_coeffs 3908111.160 1645.484377 12 6 P-C_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1897159.056 1165.116525 12 6 P-N_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 1316590.401 1026.290564 12 6 P-O_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6025893.897 2195.612698 12 6 P-P_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 4512698.060 1900.041696 12 6 P-S_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 49816.168 112.261323 12 6 P-H_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 8365.797 38.684871 12 6 P-f_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 695713.424 593.301140 12 6 P-F_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 6043158.116 2383.124568 12 6 P-c_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 10104579.020 3357.639050 12 6 P-b_non-bond-parameters/Cn,Cm,n,m nbp_coeffs 20582723.561 5230.264891 12 6 P-I_non-bond-parameters/Cn,Cm,n,m S.map I am not sure how to apply this to my model. Thank you for any help in advance. Cheers, Charlie Chand University of California, San Diego 9500 Gilman Drive La Jolla CA 92093 From owner-chemistry@ccl.net Thu Aug 3 12:34:00 2006 From: "Patrick Pang skpang,ctimail.com" To: CCL Subject: CCL:G: force constants in the G03 "frequency" output file Message-Id: <-32336-060803105727-4049-/nTmudLhDa9AlaIJWlFDdw~~server.ccl.net> X-Original-From: "Patrick Pang" Date: Thu, 3 Aug 2006 10:57:27 -0400 Sent to CCL by: "Patrick Pang" [skpang%a%ctimail.com] I employ UB98/AUG-cc-pVDZ to calculate the hydrogen molecule using G03. After optimizing the geometry, the distance between two hydrogen atoms is 0.7587 angstrom. Then I perform the frequency calculation, and the output for the force constant is 11.3961 mDyne/angstrom (1139.61 N/m) extracted from: 1 SGG Frequencies -- 4380.8712 Red. masses -- 1.0078 Frc consts -- 11.3961 IR Inten -- .0000 Atom AN X Y Z 1 1 .00 .00 .71 2 1 .00 .00 -.71 The force constant in internal coordinates from the same output file is: 1 1 .365989D+00 It is equal to 569.81 N/m, and it is a half of the value of 1139.61 N/m. I also use the change in potential energy to calculate the force constant. The electronic energy of optimized structure is -1.1707171 hartree. The electronic energy of the structure for -0.01 angstrom (i.e. 0.7587 - 0.01) is -1.1706508 hartree. The electronic energy of the structure for +0.01 angstrom (i.e. 0.7587 + 0.01) is -1.1706527 hartree. Because of the potential energy U = 1/2 k x^2, the average force constant (average of force constants calculated from the average of the force constant for 0 <-> +0.01 angstrom and the force constant for 0 <-> -0.01 angstrom) is 569.82 N/m. It is also a half of the value of 1139.61 N/m. I further use the "force" keyword to calculate the internal coodinate force for +0.01 angstrom is -0.006728 hartree/bohr. The internal coodinate force for -0.01 angstrom is +0.007144 hartree/bohr. From the equation F = - k x, the force constant is 570.20 N/m, which is the half of the value of 1139.61 N/m. Why there are two different force constant values? Thank you for your attention. If anyone know the answer, please send to skpang^_^ctimail.com Patrick Pang From owner-chemistry@ccl.net Thu Aug 3 22:30:00 2006 From: "Keith Butler keeeto2000(!)yahoo.co.uk" To: CCL Subject: CCL:G: Implimenting RM1 Method In Gaussian 03 Message-Id: <-32337-060803105727-12345-Nr59vVWlcOGoyMEUytH+zg/./server.ccl.net> X-Original-From: Keith Butler Date: Thu, 3 Aug 2006 12:36:35 +0100 (BST) Sent to CCL by: Keith Butler [keeeto2000- -yahoo.co.uk] I have succesfully impimented the RM1 method in Gaussian 03. All values which need to be changed can be found under the heading : START OF AM1 PARAMETERS in the utilam.F file in the g03 directory. The spread sheet of all of the values which need to be changed can be found at: http://www.ccl.net/cca/data/RM1_in_Gaussian03 My preliminary results with the method show significant improvements over AM1 methods, in particular for guanidinium systems, and in general pi-systems involving N atoms. Keith T. Butler [Message was modified by CCL Administrator]