Remarks gvn_xplor_top.txt Remarks Created by XPLO2D V. 050802/3.3.2 at Sat Mar 1 04:10:45 2008 for A. Nonymous Remarks Auto-generated by XPLO2D from file gvn_msd.pdb Remarks You *MUST* check/edit MASSes and CHARges !!! Remarks Check DONOrs and ACCEptors Remarks Verify IMPRopers yourself Remarks DIHEdrals which are not flat are commented out set echo=false end { Note: edit masses if necessary } MASS N_1 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_2 14.02700 ! assuming C -> 12.01100 + 1.008 * 2 (Hs) MASS C_3 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_4 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_5 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_6 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_7 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS CL_8 35.45300 ! assuming CL -> 35.45300 + 1.008 * 0 (Hs) MASS C_9 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_10 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_11 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_12 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_13 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_14 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_15 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_16 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS C_17 12.01100 ! assuming C -> 12.01100 + 1.008 * 0 (Hs) MASS C_18 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) MASS N_19 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS N_20 15.01500 ! assuming N -> 14.00700 + 1.008 * 1 (Hs) MASS C_21 13.01900 ! assuming C -> 12.01100 + 1.008 * 1 (Hs) autogenerate angles=true end RESIdue GVN { Note: electrostatics should normally not be used in } { crystallographic refinement since it can produce } { artefacts. For this reason, all charges are set to } { zero by default. Edit them if necessary } GROUp ATOM N1 TYPE N_1 CHARge 0.0 END ! Nr of Hs = 1 ATOM C2 TYPE C_2 CHARge 0.0 END ! Nr of Hs = 2 ATOM C3 TYPE C_3 CHARge 0.0 END ! Nr of Hs = 1 ATOM C4 TYPE C_4 CHARge 0.0 END ! Nr of Hs = 0 ATOM C5 TYPE C_5 CHARge 0.0 END ! Nr of Hs = 1 ATOM C6 TYPE C_6 CHARge 0.0 END ! Nr of Hs = 1 ATOM C7 TYPE C_7 CHARge 0.0 END ! Nr of Hs = 0 ATOM CL8 TYPE CL_8 CHARge 0.0 END ! Nr of Hs = 0 ATOM C9 TYPE C_9 CHARge 0.0 END ! Nr of Hs = 1 ATOM C10 TYPE C_10 CHARge 0.0 END ! Nr of Hs = 1 ATOM C11 TYPE C_11 CHARge 0.0 END ! Nr of Hs = 0 ATOM C12 TYPE C_12 CHARge 0.0 END ! Nr of Hs = 1 ATOM C13 TYPE C_13 CHARge 0.0 END ! Nr of Hs = 1 ATOM C14 TYPE C_14 CHARge 0.0 END ! Nr of Hs = 0 ATOM C15 TYPE C_15 CHARge 0.0 END ! Nr of Hs = 1 ATOM C16 TYPE C_16 CHARge 0.0 END ! Nr of Hs = 1 ATOM C17 TYPE C_17 CHARge 0.0 END ! Nr of Hs = 0 ATOM C18 TYPE C_18 CHARge 0.0 END ! Nr of Hs = 1 ATOM N19 TYPE N_19 CHARge 0.0 END ! Nr of Hs = 1 ATOM N20 TYPE N_20 CHARge 0.0 END ! Nr of Hs = 1 ATOM C21 TYPE C_21 CHARge 0.0 END ! Nr of Hs = 1 BOND N1 C2 BOND C2 C3 BOND C3 C4 BOND C3 C11 BOND C4 C5 BOND C4 C10 BOND C5 C6 BOND C6 C7 BOND C7 CL8 BOND C7 C9 BOND C9 C10 BOND C11 C12 BOND C11 C16 BOND C12 C13 BOND C13 C14 BOND C14 C15 BOND C14 C17 BOND C15 C16 BOND C17 C18 BOND C17 C21 BOND C18 N19 BOND N19 N20 BOND N20 C21 { Note: edit these DIHEdrals if necessary } DIHEdral N1 C2 C3 C4 ! flat ? (180 degrees = trans) 171.27 ! DIHEdral N1 C2 C3 C11 ! flexible dihedral ??? -59.40 ! DIHEdral C2 C3 C11 C12 ! flexible dihedral ??? 114.41 ! DIHEdral C2 C3 C11 C16 ! flexible dihedral ??? -65.56 ! DIHEdral C4 C3 C11 C12 ! flexible dihedral ??? -116.45 ! DIHEdral C4 C3 C11 C16 ! flexible dihedral ??? 63.58 DIHEdral C3 C4 C5 C6 ! flat ? (180 degrees = trans) 179.96 DIHEdral C10 C4 C5 C6 ! flat ? (0 degrees = cis) 0.00 DIHEdral C3 C4 C10 C9 ! flat ? (180 degrees = trans) 180.04 DIHEdral C5 C4 C10 C9 ! flat ? (0 degrees = cis) 0.00 DIHEdral C4 C5 C6 C7 ! flat ? (0 degrees = cis) 0.00 DIHEdral C5 C6 C7 CL8 ! flat ? (180 degrees = trans) 179.98 DIHEdral C5 C6 C7 C9 ! flat ? (0 degrees = cis) -0.01 DIHEdral C6 C7 C9 C10 ! flat ? (0 degrees = cis) 0.01 DIHEdral CL8 C7 C9 C10 ! flat ? (180 degrees = trans) 180.01 DIHEdral C7 C9 C10 C4 ! flat ? (0 degrees = cis) 0.00 DIHEdral C3 C11 C12 C13 ! flat ? (180 degrees = trans) 179.95 DIHEdral C16 C11 C12 C13 ! flat ? (0 degrees = cis) -0.08 DIHEdral C3 C11 C16 C15 ! flat ? (180 degrees = trans) 180.02 DIHEdral C12 C11 C16 C15 ! flat ? (0 degrees = cis) 0.06 DIHEdral C11 C12 C13 C14 ! flat ? (0 degrees = cis) 0.11 DIHEdral C12 C13 C14 C15 ! flat ? (0 degrees = cis) -0.11 DIHEdral C12 C13 C14 C17 ! flat ? (180 degrees = trans) 179.97 DIHEdral C13 C14 C15 C16 ! flat ? (0 degrees = cis) 0.08 DIHEdral C17 C14 C15 C16 ! flat ? (180 degrees = trans) 180.01 DIHEdral C14 C15 C16 C11 ! flat ? (0 degrees = cis) -0.06 DIHEdral C14 C17 C18 N19 ! flat ? (180 degrees = trans) 180.05 DIHEdral C21 C17 C18 N19 ! flat ? (0 degrees = cis) 0.04 DIHEdral C14 C17 C21 N20 ! flat ? (180 degrees = trans) 179.98 DIHEdral C18 C17 C21 N20 ! flat ? (0 degrees = cis) 0.00 DIHEdral C17 C18 N19 N20 ! flat ? (0 degrees = cis) -0.07 DIHEdral C18 N19 N20 C21 ! flat ? (0 degrees = cis) 0.07 DIHEdral N19 N20 C21 C17 ! flat ? (0 degrees = cis) -0.04 { Note: edit these IMPRopers if necessary } IMPRoper C3 C2 C4 C11 ! chirality or flatness improper -28.72 IMPRoper C4 C3 C5 C10 ! chirality or flatness improper -0.02 IMPRoper C7 C6 CL8 C9 ! chirality or flatness improper 0.00 IMPRoper C11 C3 C12 C16 ! chirality or flatness improper 0.02 IMPRoper C14 C13 C15 C17 ! chirality or flatness improper 0.04 IMPRoper C17 C14 C18 C21 ! chirality or flatness improper 0.01 { Note: edit any DONOrs and ACCEptors if necessary } ! DONOr H?1 N1 ! DONOr H?1 N19 ! DONOr H?1 N20 END { RESIdue GVN }