Sat Oct 15 11:25:47 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 15 2011 at 11:25:47 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6052465 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): -0.7270000 58.09200 ymin,ymax (A): -24.23900 26.94800 zmin,zma (A): -9.947001 45.00600 x,y,z range (A): 58.81900 51.18700 54.95300 scale (grids/A): 0.6052465 object centre (A): 28.68250 1.354500 17.52950 number of atom coordinates read : 3221 total number of charged atoms : 3075 net assigned charge : 5.500013 assigned positive charge : 481.5679 centred at (gu) : 91.79041 89.33646 90.00868 assigned negative charge : -476.0692 centred at (gu) : 91.81819 89.39287 89.96017 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7748 nv = 96 ne = 84 npr = 66476 no. pairs analyzed = 66476 no. exposed pairs = 3641 no. arc points = 25630 no. surface atoms = 1236 nbur = 1985 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 4448 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2585 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3327440E-10 5.3259850E-09 midg,1,midg; midg,igrid,midg 6.6444414E-09 -1.4043444E-10 1,midg,midg; igrid,midg,midg 2.8627933E-09 1.9227033E-09 gauss-seidel spectral radius is 0.9859166 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 11:25:48 rms-change max change #iterations 0.1259029 16.22821 at 10iterations 1.1165359E-02 1.487428 at 20iterations 1.0106168E-03 0.1724749 at 30iterations 1.0145541E-04 1.5260935E-02 at 40iterations 1.2460857E-05 1.7757416E-03 at 50iterations finished qdiffx linear iterations at : 11:25:51 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.2460857E-05 1.7757416E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 11:25:51 3.592u 0.221s 0:04.25 89.6% 0+0k 0+0io 6pf+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 15 2011 at 11:25:52 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.815740 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): -0.7270000 58.09200 ymin,ymax (A): -24.23900 26.94800 zmin,zma (A): -9.947001 45.00600 x,y,z range (A): 58.81900 51.18700 54.95300 scale (grids/A): 1.815740 object centre (A): 28.68250 1.354500 17.52950 number of atom coordinates read : 3221 total number of charged atoms : 3075 net assigned charge : 5.500013 assigned positive charge : 481.5679 centred at (gu) : 95.37029 88.00863 90.02473 assigned negative charge : -476.0692 centred at (gu) : 95.45435 88.17806 89.88033 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25630 grid for indexing accessible points = 1.400000 m= 29680 mr = 60027 m= 3969 mr = 22152 m= 154 mr = 2439 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1826 time to turn everything in is 0.4000000 number of dielectric boundary points 33571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 23997 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) : 0.6052465 object centre at (A) : 28.68250 1.354500 17.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0243644E-05 -1.2446022E-02 midg,1,midg; midg,igrid,midg 6.5168198E-03 5.5801435E-03 1,midg,midg; igrid,midg,midg 4.0955067E-02 2.7951567E-02 gauss-seidel spectral radius is 0.9985563 estimated iterations to convergence 209 setup time was (sec) 0.6700000 now iterating at: 11:25:53 rms-change max change #iterations 4.309366 162.1369 at 10iterations 1.973592 65.47942 at 20iterations 0.9057900 27.04151 at 30iterations 0.4151767 12.41069 at 40iterations 0.1904077 5.480766 at 50iterations 8.7578535E-02 2.672501 at 60iterations 4.0224969E-02 1.239825 at 70iterations 1.8471023E-02 0.5460427 at 80iterations 8.4699476E-03 0.2863197 at 90iterations 3.9093127E-03 0.1176758 at 100iterations 1.7887902E-03 5.4195404E-02 at 110iterations 8.2050846E-04 2.3343086E-02 at 120iterations finished qdiffx linear iterations at : 11:26:06 total time elapsed so far: 8.740000 # loops : 120 mean,max change (kT/e) : 8.2050846E-04 2.3343086E-02 energy calculations done at 8.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.860000 DelPhi exited at 11:26:07 8.864u 0.310s 0:15.77 58.1% 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 15 2011 at 11:26:07 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.723609 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): -0.7270000 58.09200 ymin,ymax (A): -24.23900 26.94800 zmin,zma (A): -9.947001 45.00600 x,y,z range (A): 58.81900 51.18700 54.95300 scale (grids/A): 2.723609 object centre (A): 28.68250 1.354500 17.52950 number of atom coordinates read : 3221 total number of charged atoms : 3075 net assigned charge : 5.500013 assigned positive charge : 481.5679 centred at (gu) : 98.05521 87.01296 90.03689 assigned negative charge : -476.0692 centred at (gu) : 98.18156 87.26697 89.82038 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 195368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25630 grid for indexing accessible points = 1.400000 m= 98251 mr = 145265 m= 33815 mr = 81251 m= 7021 mr = 27332 m= 734 mr = 5162 m= 19 mr = 440 m= 0 mr = 5 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 6460 time to turn everything in is 1.040000 number of dielectric boundary points 75753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 24592 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) : 1.815740 object centre at (A) : 28.68250 1.354500 17.52950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7987840E-02 -0.2191511 midg,1,midg; midg,igrid,midg -3.8341541E-02 8.1092499E-02 1,midg,midg; igrid,midg,midg 0.4911280 0.3546334 gauss-seidel spectral radius is 0.9992489 estimated iterations to convergence 288 setup time was (sec) 1.280000 now iterating at: 11:26:09 rms-change max change #iterations 10.31436 288.4413 at 10iterations 5.989547 121.2976 at 20iterations 3.465064 68.23430 at 30iterations 1.989120 38.65953 at 40iterations 1.146933 20.69711 at 50iterations 0.6570356 11.05006 at 60iterations 0.3775756 7.251992 at 70iterations 0.2164652 3.688448 at 80iterations 0.1238961 2.230597 at 90iterations 7.1178079E-02 1.235142 at 100iterations 4.0660888E-02 0.6946478 at 110iterations 2.3268655E-02 0.4278155 at 120iterations 1.3326511E-02 0.2352467 at 130iterations 7.6387036E-03 0.1372252 at 140iterations 4.3753278E-03 7.7053070E-02 at 150iterations 2.5070477E-03 4.6478271E-02 at 160iterations 1.4353467E-03 2.6520729E-02 at 170iterations 8.2366972E-04 1.4554977E-02 at 180iterations finished qdiffx linear iterations at : 11:26:21 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 8.2366972E-04 1.4554977E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 11:26:21 13.372u 0.232s 0:14.02 97.0% 0+0k 0+0io 0pf+0w