Mon Oct 10 23:39:22 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 23:39:22 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5697733 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): 11.33400 64.66300 ymin,ymax (A): -3.434000 59.04700 zmin,zma (A): 10.96400 54.18900 x,y,z range (A): 53.32900 62.48100 43.22500 scale (grids/A): 0.5697733 object centre (A): 37.99850 27.80650 32.57650 number of atom coordinates read : 2656 total number of charged atoms : 2515 net assigned charge : 8.000015 assigned positive charge : 400.4487 centred at (gu) : 88.83859 91.28582 89.87460 assigned negative charge : -392.4493 centred at (gu) : 88.81747 91.10955 90.00359 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5639 nv = 96 ne = 84 npr = 52911 no. pairs analyzed = 52911 no. exposed pairs = 3186 no. arc points = 22594 no. surface atoms = 1081 nbur = 1575 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 253 mr = 3087 m= 0 mr = 16 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 2789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2234 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7154 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0151248E-09 -5.9525246E-10 midg,1,midg; midg,igrid,midg -9.3231090E-10 4.8366231E-09 1,midg,midg; igrid,midg,midg 1.1628072E-09 1.1260678E-09 gauss-seidel spectral radius is 0.9840769 estimated iterations to convergence 65 setup time was (sec) 0.5400000 now iterating at: 23:39:23 rms-change max change #iterations 8.6849347E-02 13.78807 at 10iterations 7.9698358E-03 1.484699 at 20iterations 1.1969298E-03 0.2739143 at 30iterations 2.9790975E-04 7.3802948E-02 at 40iterations 7.9283760E-05 1.9939423E-02 at 50iterations finished qdiffx linear iterations at : 23:39:25 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 7.9283760E-05 1.9939423E-02 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 23:39:26 3.311u 0.157s 0:04.03 85.8% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 23:39:26 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.709320 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): 11.33400 64.66300 ymin,ymax (A): -3.434000 59.04700 zmin,zma (A): 10.96400 54.18900 x,y,z range (A): 53.32900 62.48100 43.22500 scale (grids/A): 1.709320 object centre (A): 37.99850 27.80650 32.57650 number of atom coordinates read : 2656 total number of charged atoms : 2515 net assigned charge : 8.000015 assigned positive charge : 400.4487 centred at (gu) : 86.51524 93.85708 89.62321 assigned negative charge : -392.4493 centred at (gu) : 86.45177 93.32831 90.01043 start vw surface at 0.2200000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 61892 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 20343 mr = 42912 m= 2481 mr = 14631 m= 64 mr = 1340 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 764 time to turn everything in is 0.5600000 number of dielectric boundary points 25893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19470 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5697733 object centre at (A) : 37.99850 27.80650 32.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8520733E-02 3.2223163E-03 midg,1,midg; midg,igrid,midg -5.8101187E-03 -7.3893713E-03 1,midg,midg; igrid,midg,midg 6.6235202E-04 1.0670838E-02 gauss-seidel spectral radius is 0.9983108 estimated iterations to convergence 193 setup time was (sec) 0.8500000 now iterating at: 23:39:27 rms-change max change #iterations 3.397462 168.8280 at 10iterations 1.459183 59.41302 at 20iterations 0.6294156 23.01924 at 30iterations 0.2710459 10.16138 at 40iterations 0.1169705 4.317802 at 50iterations 5.0874688E-02 1.812301 at 60iterations 2.2076650E-02 0.9099579 at 70iterations 9.7155645E-03 0.3618698 at 80iterations 4.4039055E-03 0.1911201 at 90iterations 2.1085364E-03 9.2437744E-02 at 100iterations 1.0791057E-03 5.0441742E-02 at 110iterations 5.8793993E-04 2.6950836E-02 at 120iterations finished qdiffx linear iterations at : 23:39:33 total time elapsed so far: 7.280000 # loops : 120 mean,max change (kT/e) : 5.8793993E-04 2.6950836E-02 energy calculations done at 7.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 23:39:34 7.475u 0.146s 0:07.98 95.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 23:39:34 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.563980 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): 11.33400 64.66300 ymin,ymax (A): -3.434000 59.04700 zmin,zma (A): 10.96400 54.18900 x,y,z range (A): 53.32900 62.48100 43.22500 scale (grids/A): 2.563980 object centre (A): 37.99850 27.80650 32.57650 number of atom coordinates read : 2656 total number of charged atoms : 2515 net assigned charge : 8.000015 assigned positive charge : 400.4487 centred at (gu) : 84.77283 95.78550 89.43459 assigned negative charge : -392.4493 centred at (gu) : 84.67756 94.99239 90.01546 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 143797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22594 grid for indexing accessible points = 1.400000 m= 68849 mr = 104623 m= 21686 mr = 55707 m= 4060 mr = 16902 m= 317 mr = 2841 m= 5 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2562 time to turn everything in is 1.160000 number of dielectric boundary points 58496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 20112 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.709320 object centre at (A) : 37.99850 27.80650 32.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2369347 6.0710024E-02 midg,1,midg; midg,igrid,midg -0.1537117 -0.4803008 1,midg,midg; igrid,midg,midg -3.5555668E-02 0.1087427 gauss-seidel spectral radius is 0.9991630 estimated iterations to convergence 273 setup time was (sec) 1.460000 now iterating at: 23:39:36 rms-change max change #iterations 8.553192 316.7773 at 10iterations 4.792748 123.8969 at 20iterations 2.684839 60.76030 at 30iterations 1.501926 32.69215 at 40iterations 0.8368905 18.93819 at 50iterations 0.4662488 9.468904 at 60iterations 0.2590139 5.205860 at 70iterations 0.1442195 3.004539 at 80iterations 8.0250956E-02 1.610541 at 90iterations 4.4562336E-02 0.9314880 at 100iterations 2.4822265E-02 0.5030746 at 110iterations 1.3846111E-02 0.2847977 at 120iterations 7.7867704E-03 0.1670227 at 130iterations 4.4082268E-03 9.6412659E-02 at 140iterations 2.5415020E-03 5.9387207E-02 at 150iterations 1.5191189E-03 3.7948608E-02 at 160iterations 9.4328373E-04 2.3395538E-02 at 170iterations 6.1405404E-04 1.6033173E-02 at 180iterations finished qdiffx linear iterations at : 23:39:46 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 6.1405404E-04 1.6033173E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 23:39:47 12.216u 0.160s 0:12.81 96.5% 0+0k 0+0io 0pf+0w