From owner-chemistry@ccl.net Tue Feb 27 12:21:01 2007 From: "neeraj misra misraneeraj]=[gmail.com" To: CCL Subject: CCL:G: frequency output Message-Id: <-33704-070227122025-2794-Kn5tvvLo2yEB7J+OeKym0Q(_)server.ccl.net> X-Original-From: "neeraj misra" Date: Tue, 27 Feb 2007 12:20:22 -0500 Sent to CCL by: "neeraj misra" [misraneeraj##gmail.com] DO WE HAVE TO SCALE THE POTENTIAL ENERGY DISTRIBUTIONS GIVEN IN THE FREQUENCY OUTPUT WHEN WE GIVE FREQ=INTERNAL AS THE ADDITIONAL KEYWORD IN A FREQUENCY CALCULATION BY GAUSSIAN O3W. I AM ATTACHING THE OUTPUT OF A FREQ CALCULATION WHICH GIVES THE NORMAL MODES ALSO.PLEASE CLARIFY THIS DOUBT. THANKS IN ADVANCE ---------------------------- ! Normal Mode 1 ! -------------------------- -------------------------- ! Name Definition Value Relative Weight (%) ! -------------------------------------------------------------------------------- ! R1 L(2,13,3,11,-2) 0.0529 3.3 ! ! R2 D(11,3,4,5) -0.0268 1.7 ! ! R3 D(11,3,4,14) -0.0633 3.9 ! ! R4 D(13,3,4,5) -0.0699 4.3 ! ! R5 D(13,3,4,14) -0.1064 6.5 ! ! R6 D(13,3,11,9) 0.0435 2.7 ! ! R7 D(13,3,11,12) 0.0378 2.3 ! ! R8 D(3,4,5,7) 0.0307 1.9 ! ! R9 D(14,4,5,6) 0.0488 3.0 ! ! R10 D(14,4,5,7) 0.065 4.0 ! ! R11 D(3,4,14,1) -0.2322 14.3 ! ! R12 D(3,4,14,15) -0.2016 12.4 ! ! R13 D(5,4,14,1) -0.2682 16.5 ! ! R14 D(5,4,14,15) -0.2376 14.6 ! ! R15 D(7,9,11,12) 0.0231 1.4 ! -------------------------------------------------------------------------------- ---------------------------- ! Normal Mode 2 ! -------------------------- -------------------------- ! Name Definition Value Relative Weight (%) ! -------------------------------------------------------------------------------- ! R1 L(2,13,3,11,-2) -0.1396 5.7 ! ! R2 D(11,3,4,5) 0.0721 3.0 ! ! R3 D(11,3,4,14) 0.041 1.7 ! ! R4 D(13,3,4,5) 0.1706 7.0 ! ! R5 D(13,3,4,14) 0.1394 5.7 ! ! R6 D(4,3,11,9) -0.0795 3.3 ! ! R7 D(4,3,11,12) -0.031 1.3 ! ! R8 D(13,3,11,9) -0.1715 7.1 ! ! R9 D(13,3,11,12) -0.123 5.1 ! ! R10 D(3,4,14,1) -0.2421 10.0 ! ! R11 D(3,4,14,15) -0.2265 9.3 ! ! R12 D(5,4,14,1) -0.2728 11.2 ! ! R13 D(5,4,14,15) -0.2573 10.6 ! ! R14 D(4,5,7,8) -0.0408 1.7 ! ! R15 D(4,5,7,9) -0.0642 2.6 ! ! A1 D(6,5,7,9) -0.0437 1.8 ! ! A2 D(5,7,9,10) 0.036 1.5 ! ! A3 D(5,7,9,11) 0.0571 2.3 ! ! A4 D(8,7,9,11) 0.0336 1.4 ! ! A5 D(7,9,11,12) -0.0345 1.4 ! ! A6 D(10,9,11,3) 0.0354 1.5 ! -------------------------------------------------------------------------------- ---------------------------- From owner-chemistry@ccl.net Tue Feb 27 20:28:01 2007 From: "Veronica Tello vtellof_-_gmail.com" To: CCL Subject: CCL: small molecule volume calculation Message-Id: <-33705-070227201149-24911-q8828sMcoFY5j+NykKRZ0Q_._server.ccl.net> X-Original-From: "Veronica Tello" Date: Tue, 27 Feb 2007 20:11:46 -0500 Sent to CCL by: "Veronica Tello" [vtellof:_:gmail.com] Greetings. I have calculated the volume of some cavities on a protein using the on-line program CASTp (keeping the 1.4 probe radius). I wish to calculate the volume of some possible ligands and compare results. I have access to HyperChem7. Using it, I get very different volume values when choosing either Van der Waals surface or Sovent-Accesible Surface. Which option is better suited in this case? Can someone recomend a different program (preferably open-access)? Thank you very much. Veronica Tello F Instituto de Quimica, UNAM vtellof,+,gmail.com