From owner-chemistry@ccl.net Mon Feb 28 00:16:00 2011 From: "Mannan K malie_03(~)yahoo.co.in" To: CCL Subject: CCL: How to open up Narrow pocket using Nmode analyses Message-Id: <-44027-110228001507-27862-ImJI+MLUsLk8Ad/+oL+cbA%%server.ccl.net> X-Original-From: "Mannan K" Date: Mon, 28 Feb 2011 00:15:05 -0500 Sent to CCL by: "Mannan K" [malie_03^-^yahoo.co.in] Hi, I have a pdb structure, which has a narrow binding pocket, The reported compounds cannot bind to this narrow binding pocket. But there are many reports of literature which confirm the binding pocket as well as the list of compounds. But similar subtype pdbs have more opened pocket, but not this. So I tried to generate more conformers, like opened active site of the pdb using Nmode analyses, But could not open up the structure to get a bound conformation with the known ligands. How to overcome this issue Mannan From owner-chemistry@ccl.net Mon Feb 28 05:05:00 2011 From: "Uttama Mukherjee uttamachemistry- -gmail.com" To: CCL Subject: CCL:G: ESP data from WFA program Message-Id: <-44028-110228050009-31382-SOlhkB9P9WCppU8pgEe8Qw!A!server.ccl.net> X-Original-From: "Uttama Mukherjee" Date: Mon, 28 Feb 2011 05:00:08 -0500 Sent to CCL by: "Uttama Mukherjee" [uttamachemistry,+,gmail.com] Dear all, I am working out on the density correction of energetic molucules via electrostatic potential (ESP)surface consideration. For that I need to run a WFA program(Felipe A. Bulat and Alejandro Toro-Labbe)for obtaining the ESP data. I have done that, the program is running smoothly (after generating a wfn file and a cubefile from gaussian03). But my problem is, the output of the WFA program where the ESP data is given, shows a zero value for the negative sigma square value and as a result the balance parameter is also zero. This should have some finite value (as seen in the output of a few WFA examples)otherwise the density correction factor will be zero which is not possible. Can you please suggest something? Is there any problem in the generation of the cubefile or anything else? Please help. The WFA program output for the ESP data comes as... Statistics for ESP Area Average Sigma^2 Pi Positive 135.007463 0.676609 0.001040 0.025186 Negative 0.000000 0.000000 0.000000 0.000000 Total 135.007463 0.676609 0.001040 0.025186 Balance parameter 0.000000 (Cross check) Average 0.676609 (Cross check) Variance 0.001040 Thanks and regards Uttama Mukherjee uttamachemistry(~)gmail.com From owner-chemistry@ccl.net Mon Feb 28 13:07:00 2011 From: "Guilherme Cordeiro guilhermecord]~[gmail.com" To: CCL Subject: CCL:G: UV-Vis bands obtained by ZIndo method Message-Id: <-44029-110228130555-3587-0gM3Dsa5f7bY7s/Q1yRB7A . server.ccl.net> X-Original-From: "Guilherme Cordeiro" Date: Mon, 28 Feb 2011 13:05:54 -0500 Sent to CCL by: "Guilherme Cordeiro" [guilhermecord/a\gmail.com] Dear Members, I obtained the theoretical absorption bands of free quercetin solvated in water by means of the semi-empirical ZIndo method in Gaussian 98W. Quercetin, like most flavonols, exhibit two major absorption bands in the UV/vis region. Band I, in the 300-500nm range, and band II for wavelength under 280nm. In fact, the calculation showed one absorption peak for Band I at 331.54nm and one peak for Band II at 277.34nm. But, according to A. Torreggiani et al, Band I should appear as two absorption peaks at 320 and 375nnm while Band II as one absorption at 260nm. What should be the reasons for obtaining only one peak in the 300-500nm region? Is there a scaling factor that I can use in order to correct the theoretical valeus? Citation: Torreggiania, A., Tambaa, M., Trincherob, A., & Bonora, S. (2005). Copper(II)Quercetin complexes in aqueous solutions: spectroscopic and kinetic properties. Journal of Molecular Structure , pp. 759-766. Thanks in advance. From owner-chemistry@ccl.net Mon Feb 28 18:25:01 2011 From: "Zijun Yu zjyu]|[lamar.colostate.edu" To: CCL Subject: CCL: opt error Message-Id: <-44030-110228182236-32342-jsbe+4iVfhSRyLv9GQKmvw++server.ccl.net> X-Original-From: "Zijun Yu" Date: Mon, 28 Feb 2011 18:22:34 -0500 Sent to CCL by: "Zijun Yu" [zjyu!A!lamar.colostate.edu] Hi, everyone I try to do a scan calculation. But after getting 18 optimized points, then the calculation died in optimizing the 19 point as below: Minotr: Closed shell wavefunction. Computing MP2/KS-MP2 derivatives. Using Z-Vector for PSCF gradient. Skipping F1 and S1 gradient terms here. IDoAtm=11111111111111111111111111111 IDoAtC=11111111 Frozen-core window. Direct CPHF calculation. Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. Requested convergence is 1.0D-10 RMS, and 1.0D-09 maximum. NewPWx=F KeepS1=T KeepF1=T KeepIn=T MapXYZ=F SortEE=F KeepMc=T. MDV= 524287874 using IRadAn= 0. Keep R1 ints in memory in canonical form, NReq=6337048. Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Solving linear equations separately, MaxMat= 0. There are 1 degrees of freedom in the 1st order CPHF. IDoFFX=0. LinEq1: Iter= 0 NonCon= 1 RMS=1.31D-02 Max=2.26D-01 AX will form 1 AO Fock derivatives at one time. LinEq1: Iter= 1 NonCon= 1 RMS=4.73D-03 Max=4.03D-02 LinEq1: Iter= 2 NonCon= 1 RMS=2.79D-03 Max=5.96D-02 LinEq1: Iter= 3 NonCon= 1 RMS=1.01D-03 Max=9.82D-03 LinEq1: Iter= 4 NonCon= 1 RMS=6.91D-04 Max=9.00D-03 LinEq1: Iter= 5 NonCon= 1 RMS=2.70D-04 Max=2.13D-03 LinEq1: Iter= 6 NonCon= 1 RMS=6.37D-05 Max=7.07D-04 LinEq1: Iter= 7 NonCon= 1 RMS=2.45D-05 Max=3.48D-04 LinEq1: Iter= 8 NonCon= 1 RMS=1.16D-05 Max=1.75D-04 LinEq1: Iter= 9 NonCon= 1 RMS=6.23D-06 Max=9.98D-05 LinEq1: Iter= 10 NonCon= 1 RMS=3.54D-06 Max=5.30D-05 LinEq1: Iter= 11 NonCon= 1 RMS=1.25D-06 Max=1.67D-05 LinEq1: Iter= 12 NonCon= 1 RMS=2.68D-07 Max=2.74D-06 LinEq1: Iter= 13 NonCon= 1 RMS=6.31D-08 Max=7.78D-07 LinEq1: Iter= 14 NonCon= 1 RMS=1.46D-08 Max=1.48D-07 LinEq1: Iter= 15 NonCon= 1 RMS=3.15D-09 Max=4.14D-08 LinEq1: Iter= 16 NonCon= 1 RMS=7.45D-10 Max=9.18D-09 LinEq1: Iter= 17 NonCon= 1 RMS=2.03D-10 Max=1.98D-09 LinEq1: Iter= 18 NonCon= 0 RMS=4.48D-11 Max=6.08D-10 Linear equations converged to 1.000D-10 1.000D-09 after 18 iterations. End of Minotr Frequency-dependent properties file 721 does not exist. End of Minotr Frequency-dependent properties file 722 does not exist. Leave Link 1002 at Mon Feb 28 16:25:05 2011, MaxMem= 524288000 cpu: 4.0 Job ran on Machine= Can anyone please tell me what is the problem?