Sun Oct 9 12:40:28 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 Sun Oct 9 2011 at 12:40:28 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 = 2396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6856307 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): -6.546000 43.94700 ymin,ymax (A): -14.31700 37.60600 zmin,zma (A): 2.315000 45.23100 x,y,z range (A): 50.49300 51.92300 42.91600 scale (grids/A): 0.6856307 object centre (A): 18.70050 11.64450 23.77300 number of atom coordinates read : 2396 total number of charged atoms : 2255 net assigned charge : 5.500014 assigned positive charge : 366.0630 centred at (gu) : 89.79634 90.96584 90.29932 assigned negative charge : -360.5636 centred at (gu) : 89.79084 91.07895 90.37490 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7603 nv = 96 ne = 84 npr = 47909 no. pairs analyzed = 47909 no. exposed pairs = 2997 no. arc points = 21075 no. surface atoms = 1008 nbur = 1388 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4162 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2062 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0617732E-08 1.4680236E-09 midg,1,midg; midg,igrid,midg 5.4811085E-08 -1.4727519E-08 1,midg,midg; igrid,midg,midg 2.6940338E-08 2.8550776E-08 gauss-seidel spectral radius is 0.9889511 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 12:40:29 rms-change max change #iterations 0.1831694 27.46218 at 10iterations 2.1546056E-02 2.621340 at 20iterations 2.8215256E-03 0.3618307 at 30iterations 5.5566343E-04 7.6784134E-02 at 40iterations 1.6519873E-04 2.6050568E-02 at 50iterations finished qdiffx linear iterations at : 12:40:32 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.6519873E-04 2.6050568E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 12:40:32 3.514u 0.204s 0:04.00 92.7% 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 Sun Oct 9 2011 at 12:40:32 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 = 2396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.056892 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): -6.546000 43.94700 ymin,ymax (A): -14.31700 37.60600 zmin,zma (A): 2.315000 45.23100 x,y,z range (A): 50.49300 51.92300 42.91600 scale (grids/A): 2.056892 object centre (A): 18.70050 11.64450 23.77300 number of atom coordinates read : 2396 total number of charged atoms : 2255 net assigned charge : 5.500014 assigned positive charge : 366.0630 centred at (gu) : 89.38857 92.89695 90.89748 assigned negative charge : -360.5636 centred at (gu) : 89.37240 93.23678 91.12440 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 30804 mr = 56207 m= 5226 mr = 22644 m= 419 mr = 3255 m= 9 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 35115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17860 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) : 0.6856307 object centre at (A) : 18.70050 11.64450 23.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7838915E-02 1.3954164E-02 midg,1,midg; midg,igrid,midg 1.2454342E-02 -2.3412842E-02 1,midg,midg; igrid,midg,midg 5.0102580E-02 4.5767641E-03 gauss-seidel spectral radius is 0.9988045 estimated iterations to convergence 229 setup time was (sec) 0.6700000 now iterating at: 12:40:33 rms-change max change #iterations 4.745009 228.1966 at 10iterations 2.321221 92.81992 at 20iterations 1.136897 36.56741 at 30iterations 0.5603486 17.65845 at 40iterations 0.2753949 7.841736 at 50iterations 0.1359975 3.934998 at 60iterations 6.6982210E-02 1.939103 at 70iterations 3.3082753E-02 0.9539833 at 80iterations 1.6448647E-02 0.4761000 at 90iterations 8.2167424E-03 0.2422180 at 100iterations 4.1654767E-03 0.1474266 at 110iterations 2.2019278E-03 6.5002441E-02 at 120iterations finished qdiffx linear iterations at : 12:40:41 total time elapsed so far: 8.590000 # loops : 120 mean,max change (kT/e) : 2.2019278E-03 6.5002441E-02 energy calculations done at 8.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.720000 DelPhi exited at 12:40:42 8.719u 0.275s 0:09.26 96.9% 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 Sun Oct 9 2011 at 12:40:42 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 = 2396 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.085338 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): -6.546000 43.94700 ymin,ymax (A): -14.31700 37.60600 zmin,zma (A): 2.315000 45.23100 x,y,z range (A): 50.49300 51.92300 42.91600 scale (grids/A): 3.085338 object centre (A): 18.70050 11.64450 23.77300 number of atom coordinates read : 2396 total number of charged atoms : 2255 net assigned charge : 5.500014 assigned positive charge : 366.0630 centred at (gu) : 89.08269 94.34527 91.34612 assigned negative charge : -360.5636 centred at (gu) : 89.05853 94.85509 91.68651 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 186748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21075 grid for indexing accessible points = 1.400000 m= 97411 mr = 135754 m= 37198 mr = 79744 m= 9605 mr = 29824 m= 1635 mr = 7033 m= 159 mr = 1052 m= 6 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 79289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 18039 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) : 2.056892 object centre at (A) : 18.70050 11.64450 23.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4524810 3.6781397E-02 midg,1,midg; midg,igrid,midg 0.3652908 -0.4023853 1,midg,midg; igrid,midg,midg 0.5167268 -0.1971691 gauss-seidel spectral radius is 0.9992932 estimated iterations to convergence 297 setup time was (sec) 1.570000 now iterating at: 12:40:44 rms-change max change #iterations 10.76701 428.5325 at 10iterations 6.374760 134.3794 at 20iterations 3.762070 75.80908 at 30iterations 2.221731 40.62668 at 40iterations 1.304348 23.82615 at 50iterations 0.7654980 14.42533 at 60iterations 0.4488467 8.349872 at 70iterations 0.2625433 4.841972 at 80iterations 0.1537114 2.520708 at 90iterations 8.9927614E-02 1.479519 at 100iterations 5.2660529E-02 0.8687916 at 110iterations 3.0896559E-02 0.5801392 at 120iterations 1.8197926E-02 0.3156776 at 130iterations 1.0840045E-02 0.2047119 at 140iterations 6.5977480E-03 0.1170158 at 150iterations 4.1297730E-03 7.9582214E-02 at 160iterations 2.7190866E-03 5.6556702E-02 at 170iterations 1.9136294E-03 4.0596008E-02 at 180iterations finished qdiffx linear iterations at : 12:40:56 total time elapsed so far: 14.46000 # loops : 180 mean,max change (kT/e) : 1.9136294E-03 4.0596008E-02 energy calculations done at 14.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.59000 DelPhi exited at 12:40:57 14.591u 0.264s 0:15.12 98.2% 0+0k 0+0io 0pf+0w