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-- Guanglei Cui State University of New York Department of Chemistry Stony Brook, 11794-3400rdparm transformed trajectory, parm was ../vic.top -15.265 4.369 -3.649 -15.943 5.048 -3.651 -17.182 4.394 -3.963 -17.176 4.249 -5.043 -18.020 5.039 -3.699 -17.357 2.995 -3.415 -18.439 2.904 -3.328 -16.828 2.015 -4.280 -16.414 0.914 -3.488 -17.258 0.280 -3.215 -15.428 0.040 -4.251 -14.798 0.587 -5.398 -15.047 1.564 -5.786 -13.847 -0.209 -6.055 -13.199 0.107 -6.860 -13.504 -1.441 -5.426 -12.579 -2.204 -5.961 -12.817 -3.173 -5.803 -12.246 -1.902 -6.865 -14.191 -1.973 -4.412 -15.124 -1.241 -3.831 -15.736 -1.909 -2.979 -16.827 2.806 -2.002 -16.325 3.701 -1.634 -15.808 1.670 -2.287 -14.862 2.167 -2.503 -15.637 1.013 -1.434 -17.890 2.268 -1.124 -17.802 2.353 0.536 -19.130 2.191 1.104 -16.989 3.555 0.830 -17.024 1.036 1.009 -17.612 -0.263 0.678 -18.510 -0.324 1.293 -17.864 -0.285 -0.382 -16.745 -1.436 1.040 -17.350 -2.335 1.159 -15.749 -1.698 0.017 -14.793 -2.496 0.590 -15.287 -3.447 0.790 -13.593 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-2.210 -9.968 -14.023 -2.005 -9.416 -14.775 -2.569 -9.988 -12.821 -2.973 -9.081 -12.874 -3.576 -10.880 -12.918 -3.591 -11.202 -14.386 -1.375 -12.550 -14.731 -2.205 -13.386 -15.643 -1.400 -12.206 -15.181 -3.526 -13.148 -13.322 -2.198 -13.675 -12.608 -1.042 -14.302 -13.218 -0.391 -12.803 -12.230 -0.507 -14.692 -11.474 -1.384 -14.956 -11.060 -0.411 -13.986 -10.432 -2.137 -14.905 -9.848 -2.973 -15.665 -9.401 -2.332 -14.236 -8.925 -3.804 -13.363 -9.167 -4.803 -13.144 -10.160 -5.168 -12.971 -8.133 -5.504 -13.520 -7.034 -4.800 -13.412 -5.586 -5.009 -12.679 -4.917 -5.793 -14.098 -4.854 -4.045 -13.957 -3.865 -4.187 -14.871 -5.426 -3.070 -15.703 -4.635 -2.406 -15.707 -3.638 -2.572 -16.551 -5.072 -2.073 -15.053 -6.762 -2.949 -14.273 -7.541 -3.779 -15.945 -11.803 -2.266 -15.952 -12.857 -2.545 -15.653 -11.101 -3.576 -14.896 -11.561 -4.211 -16.561 -10.769 -4.080 -17.233 -11.403 -1.758 -17.885 -11.343 -2.460 #!/usr/bin/tcsh # Example script to run a MD trajectories whose coordinate # format is GROMOS. All irrelevent variables are commented out. # Read the manuals for further explanation. setenv status On # setenv Program progress - On setenv dna_or_protein dna #Is it DNA or Protein? # setenv nresidue #Number of residues- relevent for protein. # setenv chain #Irrelevent for DNA. For Protein, the chain # #name # setenv start_residue #In case of proteins, the residue to start the # #analysis from. # setenv end_residue #In case of proteins, the residue to end the # #analysis at. setenv nucleotide 10 #Number of nucleotide units/strand. setenv sequence "CCAACGTTGG" #setenv sequence "CGAACG" #One letter nucleotide sequence for the left #hand strand only setenv insert_into_bdna no #Read the manual for insertion into setenv insert_into_adna no #straight helical axes. setenv frequency 1 #Choose every frequency'th structure for # #analysis. # setenv distance_tolerance #Used in determining connectivities. # #If you get errors about missing # #connectivities, increase this slightly, # # setenv upto .4. If problems exist even after # #that, check your coordinates. setenv include_first no #Show the values for the first structure in # #the graphics. setenv draw_structures plate #Create strn.pdb files with just the plates. setenv drawing_type dynamics #Use dynamics data structure. setenv user_notes "Vickie Structure Results" #Some notes. setenv coord_format pdb #The file is in PDB format. setenv additional_file_format Dynamics #Additional file is in COR format. setenv do_plotting yes # Don't do the graphics now. # #I wish to edit the winlim.dat from the # #dials_and_windows before producing graphics. setenv layout 0 #Use the layout0.dat file. #setenv device #set the device to Post, for example. setenv start_time 0. #First structure corresponds to 20 ps setenv time_interval 2. #Every subsequent structure is after 20ps. # setenv canonical_dials #All these default to YES. # setenv canonical_helics #Which means, All canonical "Dials" and # setenv canonical_junctions #"Windows" will be drawn. # setenv minmax_dials #All these default to NO. # setenv minmax_helics # setenv minmax_junctions #Don't show average or min and max values. # setenv average_dials # setenv average_helics # setenv average_junctions #Upto here. # setenv labels #I don't want any labels. # setenv patterns #No patterns also. # setenv canonical_patterns #No to this one too. # setenv draw_dials #The next three default to yes, meaning # setenv draw_helics #draw all the dials and windows. # setenv draw_junctions #Set them to "No" if you want. setenv for007 ../../r/massaged.pdb #I wish to analyze the Dickerson crystal setenv for008 ../md5.21st #Dynamics results. dials_and_windows #I have the defined PATH to include the Attachment Converted: "c:\eudora\attach\massaged.pdb"Received on Wed Jun 07 2000 - 08:54:34 PDT