Sat Oct 8 13:55:29 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 Sat Oct 8 2011 at 13:55:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: NDP 350 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6336210 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): 14.75300 70.93800 ymin,ymax (A): 11.49200 56.23400 zmin,zma (A): -11.28700 44.53700 x,y,z range (A): 56.18501 44.74200 55.82400 scale (grids/A): 0.6336210 object centre (A): 42.84550 33.86300 16.62500 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -1.999993 assigned positive charge : 451.7716 centred at (gu) : 91.70158 90.38318 88.82383 assigned negative charge : -453.7722 centred at (gu) : 91.63789 90.47687 88.78129 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8008 nv = 96 ne = 84 npr = 63128 no. pairs analyzed = 63128 no. exposed pairs = 3527 no. arc points = 24184 no. surface atoms = 1194 nbur = 1824 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4611 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4500000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2384 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 9808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.4292361E-09 1.8256106E-09 midg,1,midg; midg,igrid,midg 7.4667543E-09 -1.4365733E-08 1,midg,midg; igrid,midg,midg -6.7499828E-09 7.0424937E-09 gauss-seidel spectral radius is 0.9871269 estimated iterations to convergence 72 setup time was (sec) 0.8000000 now iterating at: 13:55:30 rms-change max change #iterations 0.1503363 22.59576 at 10iterations 1.4777042E-02 2.012035 at 20iterations 1.4461215E-03 0.1782608 at 30iterations 1.4452219E-04 1.7765045E-02 at 40iterations 1.5535841E-05 2.0561218E-03 at 50iterations finished qdiffx linear iterations at : 13:55:34 total time elapsed so far: 4.760000 # loops : 50 mean,max change (kT/e) : 1.5535841E-05 2.0561218E-03 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 13:55:35 4.990u 0.475s 0:05.84 93.4% 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 Sat Oct 8 2011 at 13:55:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: NDP 350 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.900863 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): 14.75300 70.93800 ymin,ymax (A): 11.49200 56.23400 zmin,zma (A): -11.28700 44.53700 x,y,z range (A): 56.18501 44.74200 55.82400 scale (grids/A): 1.900863 object centre (A): 42.84550 33.86300 16.62500 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -1.999993 assigned positive charge : 451.7716 centred at (gu) : 95.10442 91.14901 86.47101 assigned negative charge : -453.7722 centred at (gu) : 94.91356 91.43015 86.34348 start vw surface at 0.1700000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 87033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24184 grid for indexing accessible points = 1.400000 m= 32059 mr = 62695 m= 5042 mr = 24076 m= 332 mr = 3113 m= 4 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 740 time to turn everything in is 0.8900000 number of dielectric boundary points 34474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 22640 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) : 0.6336210 object centre at (A) : 42.84550 33.86300 16.62500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4915780E-02 6.7847949E-03 midg,1,midg; midg,igrid,midg 1.1337776E-02 -2.8597072E-03 1,midg,midg; igrid,midg,midg -1.9488195E-02 8.1281550E-03 gauss-seidel spectral radius is 0.9986622 estimated iterations to convergence 217 setup time was (sec) 1.230000 now iterating at: 13:55:36 rms-change max change #iterations 4.620249 185.2139 at 10iterations 2.185848 69.62466 at 20iterations 1.033807 30.30622 at 30iterations 0.4880992 13.83860 at 40iterations 0.2306824 6.794579 at 50iterations 0.1091284 3.555954 at 60iterations 5.1524878E-02 1.537687 at 70iterations 2.4360102E-02 0.6797390 at 80iterations 1.1508657E-02 0.3295240 at 90iterations 5.4480885E-03 0.1756144 at 100iterations 2.5780450E-03 7.8800201E-02 at 110iterations 1.2218379E-03 3.5175323E-02 at 120iterations finished qdiffx linear iterations at : 13:55:47 total time elapsed so far: 11.46000 # loops : 120 mean,max change (kT/e) : 1.2218379E-03 3.5175323E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 13:55:47 11.699u 0.510s 0:12.55 97.2% 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 Sat Oct 8 2011 at 13:55:47 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3018 !!! WARNING: NDP 350 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.851295 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): 14.75300 70.93800 ymin,ymax (A): 11.49200 56.23400 zmin,zma (A): -11.28700 44.53700 x,y,z range (A): 56.18501 44.74200 55.82400 scale (grids/A): 2.851295 object centre (A): 42.84550 33.86300 16.62500 number of atom coordinates read : 3018 total number of charged atoms : 2871 net assigned charge : -1.999993 assigned positive charge : 451.7716 centred at (gu) : 97.65621 91.72342 84.70632 assigned negative charge : -453.7722 centred at (gu) : 97.37010 92.14520 84.51518 start vw surface at 0.1600000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 201809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24184 grid for indexing accessible points = 1.400000 m= 104343 mr = 151787 m= 37909 mr = 86663 m= 9021 mr = 30568 m= 1310 mr = 6649 m= 86 mr = 881 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 2606 time to turn everything in is 2.330000 number of dielectric boundary points 77908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 22966 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) : 1.900863 object centre at (A) : 42.84550 33.86300 16.62500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6405026 0.1199986 midg,1,midg; midg,igrid,midg 0.1210879 4.9240431E-03 1,midg,midg; igrid,midg,midg -7.5984187E-02 0.1414027 gauss-seidel spectral radius is 0.9992694 estimated iterations to convergence 292 setup time was (sec) 2.720000 now iterating at: 13:55:50 rms-change max change #iterations 10.76755 419.4899 at 10iterations 6.310912 139.2408 at 20iterations 3.672049 69.79458 at 30iterations 2.138814 38.48653 at 40iterations 1.240951 24.25563 at 50iterations 0.7186162 12.91271 at 60iterations 0.4155183 7.595830 at 70iterations 0.2400556 3.867676 at 80iterations 0.1389713 2.761522 at 90iterations 8.0177113E-02 1.333469 at 100iterations 4.6360586E-02 0.7519016 at 110iterations 2.6773680E-02 0.4674206 at 120iterations 1.5420359E-02 0.2416553 at 130iterations 8.9297900E-03 0.1465340 at 140iterations 5.1398682E-03 8.8318706E-02 at 150iterations 2.9665423E-03 4.8284531E-02 at 160iterations 1.7123561E-03 2.8024197E-02 at 170iterations 9.8673766E-04 1.7239571E-02 at 180iterations finished qdiffx linear iterations at : 13:56:08 total time elapsed so far: 20.02000 # loops : 180 mean,max change (kT/e) : 9.8673766E-04 1.7239571E-02 energy calculations done at 20.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.23000 DelPhi exited at 13:56:08 20.234u 0.550s 0:21.06 98.6% 0+0k 0+0io 0pf+0w