Mon Oct 10 13:55:04 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 13:55:04 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 = 3162 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: 0.5615053 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): -47.04200 7.225000 ymin,ymax (A): 175.5460 237.0430 zmin,zma (A): 78.41500 141.8160 x,y,z range (A): 54.26700 61.49701 63.40101 scale (grids/A): 0.5615053 object centre (A): -19.90850 206.2945 110.1155 number of atom coordinates read : 3162 total number of charged atoms : 3023 net assigned charge : 15.50002 assigned positive charge : 464.8328 centred at (gu) : 90.27309 89.48395 90.27802 assigned negative charge : -449.3344 centred at (gu) : 90.19839 89.40166 90.39484 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6855 nv = 96 ne = 84 npr = 60450 no. pairs analyzed = 60450 no. exposed pairs = 4409 no. arc points = 31636 no. surface atoms = 1455 nbur = 1707 mkacc time = 0.1000000 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= 301 mr = 3331 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2200000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3244 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8730 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9136871E-09 3.7088183E-10 midg,1,midg; midg,igrid,midg 8.6259250E-10 2.4024143E-09 1,midg,midg; igrid,midg,midg 8.1119678E-10 2.8037819E-09 gauss-seidel spectral radius is 0.9836697 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 13:55:05 rms-change max change #iterations 8.3180539E-02 14.77666 at 10iterations 5.7692691E-03 0.9023895 at 20iterations 4.5321471E-04 7.1358204E-02 at 30iterations 4.5159512E-05 6.7596436E-03 at 40iterations 7.1562890E-06 1.0743141E-03 at 50iterations finished qdiffx linear iterations at : 13:55:08 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.1562890E-06 1.0743141E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 13:55:09 3.357u 0.187s 0:04.13 85.4% 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 Mon Oct 10 2011 at 13:55:10 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 = 3162 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.684516 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): -47.04200 7.225000 ymin,ymax (A): 175.5460 237.0430 zmin,zma (A): 78.41500 141.8160 x,y,z range (A): 54.26700 61.49701 63.40101 scale (grids/A): 1.684516 object centre (A): -19.90850 206.2945 110.1155 number of atom coordinates read : 3162 total number of charged atoms : 3023 net assigned charge : 15.50002 assigned positive charge : 464.8328 centred at (gu) : 90.81823 88.45091 90.83313 assigned negative charge : -449.3344 centred at (gu) : 90.59496 88.20449 91.18428 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31636 grid for indexing accessible points = 1.400000 m= 23698 mr = 48863 m= 2708 mr = 15777 m= 85 mr = 1245 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1176 time to turn everything in is 0.3600000 number of dielectric boundary points 35391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 338 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 23285 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) : 0.5615053 object centre at (A) : -19.90850 206.2945 110.1155 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2141479E-03 6.1503067E-03 midg,1,midg; midg,igrid,midg 4.7593862E-03 2.7827211E-02 1,midg,midg; igrid,midg,midg 9.0094674E-03 1.7579125E-02 gauss-seidel spectral radius is 0.9983443 estimated iterations to convergence 195 setup time was (sec) 0.5900000 now iterating at: 13:55:11 rms-change max change #iterations 3.599126 167.4261 at 10iterations 1.548117 54.79745 at 20iterations 0.6674095 23.78492 at 30iterations 0.2889950 10.25787 at 40iterations 0.1245605 5.167755 at 50iterations 5.3817999E-02 1.797148 at 60iterations 2.3318727E-02 0.8102722 at 70iterations 1.0104272E-02 0.3375931 at 80iterations 4.3830532E-03 0.1475143 at 90iterations 1.8958161E-03 7.4591637E-02 at 100iterations 8.2403584E-04 3.0738831E-02 at 110iterations 3.5852668E-04 1.1894166E-02 at 120iterations finished qdiffx linear iterations at : 13:55:18 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 3.5852668E-04 1.1894166E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 13:55:19 8.016u 0.230s 0:08.58 96.0% 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 13:55:36 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 = 3162 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: 2.526774 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): -47.04200 7.225000 ymin,ymax (A): 175.5460 237.0430 zmin,zma (A): 78.41500 141.8160 x,y,z range (A): 54.26700 61.49701 63.40101 scale (grids/A): 2.526774 object centre (A): -19.90850 206.2945 110.1155 number of atom coordinates read : 3162 total number of charged atoms : 3023 net assigned charge : 15.50002 assigned positive charge : 464.8328 centred at (gu) : 91.22713 87.67616 91.24937 assigned negative charge : -449.3344 centred at (gu) : 90.89249 87.30691 91.77634 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 173322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31636 grid for indexing accessible points = 1.400000 m= 80295 mr = 120122 m= 24072 mr = 61988 m= 4244 mr = 17571 m= 316 mr = 2650 m= 4 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 4307 time to turn everything in is 0.9000000 number of dielectric boundary points 79792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 24174 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) : 1.684516 object centre at (A) : -19.90850 206.2945 110.1155 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1975460 0.1065116 midg,1,midg; midg,igrid,midg -0.2660748 0.4249549 1,midg,midg; igrid,midg,midg 0.1343458 0.1872138 gauss-seidel spectral radius is 0.9992059 estimated iterations to convergence 280 setup time was (sec) 1.140000 now iterating at: 13:55:37 rms-change max change #iterations 9.185224 303.8695 at 10iterations 5.327692 138.8651 at 20iterations 3.061971 68.64304 at 30iterations 1.753397 38.97745 at 40iterations 1.001346 21.52560 at 50iterations 0.5702671 12.25499 at 60iterations 0.3231168 6.812737 at 70iterations 0.1831259 3.697683 at 80iterations 0.1034593 2.296082 at 90iterations 5.8533955E-02 1.154015 at 100iterations 3.3038210E-02 0.6658936 at 110iterations 1.8630384E-02 0.3906174 at 120iterations 1.0480518E-02 0.1866365 at 130iterations 5.9164562E-03 0.1174431 at 140iterations 3.3363770E-03 5.9656143E-02 at 150iterations 1.8767747E-03 4.0119648E-02 at 160iterations 1.0571347E-03 2.0126343E-02 at 170iterations 5.9591286E-04 1.1541843E-02 at 180iterations finished qdiffx linear iterations at : 13:55:49 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 5.9591286E-04 1.1541843E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 13:55:50 12.926u 0.257s 0:13.54 97.2% 0+0k 0+0io 0pf+0w