Sun Oct 9 19:01:53 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+sph2.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 = amb2.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 19:01:54 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5374 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5488153 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): 3.255000 68.12200 ymin,ymax (A): -8.978000 53.29900 zmin,zma (A): -0.9480000 63.40200 x,y,z range (A): 64.86700 62.27700 64.35000 scale (grids/A): 0.5488153 object centre (A): 35.68850 22.16050 31.22700 number of atom coordinates read : 5374 total number of charged atoms : 5215 net assigned charge : -0.4509439 assigned positive charge : 829.0339 centred at (gu) : 88.28064 89.19852 89.20226 assigned negative charge : -829.4912 centred at (gu) : 88.16213 89.22298 89.13270 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10455 nv = 96 ne = 84 npr = 109987 no. pairs analyzed = 109987 no. exposed pairs = 6165 no. arc points = 42248 no. surface atoms = 2091 nbur = 3283 mkacc time = 0.1800000 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 = 1.568000 m= 481 mr = 6008 m= 0 mr = 36 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4265 ## 496 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 13817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1669856E-09 7.7978379E-10 midg,1,midg; midg,igrid,midg 4.1760520E-10 -2.7003855E-10 1,midg,midg; igrid,midg,midg -2.5372024E-09 1.0487751E-09 gauss-seidel spectral radius is 0.9830519 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 19:01:54 rms-change max change #iterations 0.1079540 12.28606 at 10iterations 9.8877288E-03 1.412449 at 20iterations 2.8413683E-03 0.3085251 at 30iterations 1.2735915E-03 0.1534761 at 40iterations 5.9637270E-04 7.7404618E-02 at 50iterations finished qdiffx linear iterations at : 19:01:57 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 5.9637270E-04 7.7404618E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 19:01:58 3.575u 0.177s 0:04.10 91.2% 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 Sun Oct 9 2011 at 19:01:58 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5374 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.646446 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): 3.255000 68.12200 ymin,ymax (A): -8.978000 53.29900 zmin,zma (A): -0.9480000 63.40200 x,y,z range (A): 64.86700 62.27700 64.35000 scale (grids/A): 1.646446 object centre (A): 35.68850 22.16050 31.22700 number of atom coordinates read : 5374 total number of charged atoms : 5215 net assigned charge : -0.4509439 assigned positive charge : 829.0339 centred at (gu) : 84.84041 87.59412 87.60553 assigned negative charge : -829.4912 centred at (gu) : 84.48638 87.66884 87.39825 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 117298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42248 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 40401 mr = 85367 m= 4712 mr = 29313 m= 136 mr = 2545 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.5600000 number of dielectric boundary points 45311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 369 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 39927 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) : 0.5488153 object centre at (A) : 35.68850 22.16050 31.22700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0824495E-02 1.4873132E-02 midg,1,midg; midg,igrid,midg 1.7998870E-02 8.1623122E-03 1,midg,midg; igrid,midg,midg -2.9691363E-02 7.3887734E-03 gauss-seidel spectral radius is 0.9984274 estimated iterations to convergence 200 setup time was (sec) 0.7700000 now iterating at: 19:01:59 rms-change max change #iterations 4.935273 168.2358 at 10iterations 2.185382 64.79285 at 20iterations 0.9726995 26.61135 at 30iterations 0.4311338 11.99119 at 40iterations 0.1915775 5.288406 at 50iterations 8.5568406E-02 2.238936 at 60iterations 3.8598329E-02 1.145187 at 70iterations 1.7789926E-02 0.5012331 at 80iterations 8.6578578E-03 0.2506027 at 90iterations 4.6956926E-03 0.1321602 at 100iterations 2.9031108E-03 8.2958221E-02 at 110iterations 2.0115802E-03 5.1834106E-02 at 120iterations finished qdiffx linear iterations at : 19:02:06 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 2.0115802E-03 5.1834106E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 19:02:06 8.150u 0.218s 0:08.68 96.3% 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 Sun Oct 9 2011 at 19:02:06 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5374 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.469669 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): 3.255000 68.12200 ymin,ymax (A): -8.978000 53.29900 zmin,zma (A): -0.9480000 63.40200 x,y,z range (A): 64.86700 62.27700 64.35000 scale (grids/A): 2.469669 object centre (A): 35.68850 22.16050 31.22700 number of atom coordinates read : 5374 total number of charged atoms : 5215 net assigned charge : -0.4509439 assigned positive charge : 829.0339 centred at (gu) : 82.26048 86.39078 86.40781 assigned negative charge : -829.4912 centred at (gu) : 81.72951 86.50320 86.09725 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 273058 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42248 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 136966 mr = 207977 m= 42742 mr = 112098 m= 7638 mr = 33137 m= 567 mr = 5239 m= 8 mr = 306 m= 0 mr = 2 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 888 time to turn everything in is 1.430000 number of dielectric boundary points 102220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 41678 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) : 1.646446 object centre at (A) : 35.68850 22.16050 31.22700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4880221 0.3578086 midg,1,midg; midg,igrid,midg 0.1862260 -1.6757178E-03 1,midg,midg; igrid,midg,midg -0.5256534 6.9619581E-02 gauss-seidel spectral radius is 0.9992549 estimated iterations to convergence 289 setup time was (sec) 1.680000 now iterating at: 19:02:08 rms-change max change #iterations 12.48892 324.5417 at 10iterations 7.344922 177.9849 at 20iterations 4.293051 86.57948 at 30iterations 2.497997 46.59918 at 40iterations 1.450443 25.62077 at 50iterations 0.8391089 13.21087 at 60iterations 0.4858990 8.077099 at 70iterations 0.2799612 4.337219 at 80iterations 0.1618107 2.531925 at 90iterations 9.3379140E-02 1.487570 at 100iterations 5.3980771E-02 0.9959097 at 110iterations 3.1293135E-02 0.5215952 at 120iterations 1.8285995E-02 0.2991791 at 130iterations 1.0933852E-02 0.1838360 at 140iterations 6.7342510E-03 0.1121292 at 150iterations 4.3625683E-03 7.3319435E-02 at 160iterations 3.0274598E-03 5.1542997E-02 at 170iterations 2.2584386E-03 3.6666870E-02 at 180iterations finished qdiffx linear iterations at : 19:02:20 total time elapsed so far: 13.60000 # loops : 180 mean,max change (kT/e) : 2.2584386E-03 3.6666870E-02 energy calculations done at 13.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.73000 DelPhi exited at 19:02:21 13.730u 0.224s 0:14.32 97.4% 0+0k 0+0io 0pf+0w