Tue Oct 11 06:10:10 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 Tue Oct 11 2011 at 06:10:10 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7137988 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): -20.06100 24.02100 ymin,ymax (A): 0.4980000 39.10000 zmin,zma (A): 19.90200 69.77600 x,y,z range (A): 44.08200 38.60200 49.87400 scale (grids/A): 0.7137988 object centre (A): 1.980000 19.79900 44.83900 number of atom coordinates read : 2004 total number of charged atoms : 1899 net assigned charge : 7.039010 assigned positive charge : 308.7841 centred at (gu) : 90.10985 90.95049 89.98406 assigned negative charge : -301.7451 centred at (gu) : 89.92058 90.92877 89.95837 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7065 nv = 96 ne = 84 npr = 39698 no. pairs analyzed = 39698 no. exposed pairs = 2489 no. arc points = 16990 no. surface atoms = 845 nbur = 1159 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4083 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1611 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7740 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4740745E-08 8.2599527E-08 midg,1,midg; midg,igrid,midg 4.7724100E-08 9.6557741E-08 1,midg,midg; igrid,midg,midg -3.6472830E-08 1.7463260E-07 gauss-seidel spectral radius is 0.9897611 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 06:10:11 rms-change max change #iterations 0.2083627 27.56178 at 10iterations 2.6448879E-02 4.045258 at 20iterations 3.4725261E-03 0.4460258 at 30iterations 5.5203546E-04 6.7245483E-02 at 40iterations 1.2496818E-04 1.6777039E-02 at 50iterations finished qdiffx linear iterations at : 06:10:15 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 1.2496818E-04 1.6777039E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 06:10:15 4.425u 0.393s 0:05.15 93.3% 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 Tue Oct 11 2011 at 06:10:15 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.141396 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): -20.06100 24.02100 ymin,ymax (A): 0.4980000 39.10000 zmin,zma (A): 19.90200 69.77600 x,y,z range (A): 44.08200 38.60200 49.87400 scale (grids/A): 2.141396 object centre (A): 1.980000 19.79900 44.83900 number of atom coordinates read : 2004 total number of charged atoms : 1899 net assigned charge : 7.039010 assigned positive charge : 308.7841 centred at (gu) : 90.32944 92.85171 89.95215 assigned negative charge : -301.7451 centred at (gu) : 89.76191 92.78645 89.87529 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16990 grid for indexing accessible points = 1.400000 m= 30563 mr = 52485 m= 5957 mr = 23188 m= 508 mr = 3911 m= 5 mr = 246 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 31268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15092 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) : 0.7137988 object centre at (A) : 1.980000 19.79900 44.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8256207E-02 6.5605268E-02 midg,1,midg; midg,igrid,midg 2.3306110E-03 3.6618292E-02 1,midg,midg; igrid,midg,midg 9.2649320E-03 4.5539677E-02 gauss-seidel spectral radius is 0.9988439 estimated iterations to convergence 233 setup time was (sec) 0.9200000 now iterating at: 06:10:16 rms-change max change #iterations 4.628264 183.1216 at 10iterations 2.303504 70.02785 at 20iterations 1.151790 39.00503 at 30iterations 0.5736316 17.41327 at 40iterations 0.2877538 9.295359 at 50iterations 0.1431236 4.335907 at 60iterations 7.1480453E-02 2.186366 at 70iterations 3.5613339E-02 1.047178 at 80iterations 1.7878357E-02 0.5265427 at 90iterations 8.9387791E-03 0.2507558 at 100iterations 4.5019942E-03 0.1488762 at 110iterations 2.2880100E-03 6.9074631E-02 at 120iterations finished qdiffx linear iterations at : 06:10:26 total time elapsed so far: 10.33000 # loops : 120 mean,max change (kT/e) : 2.2880100E-03 6.9074631E-02 energy calculations done at 10.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.49000 DelPhi exited at 06:10:26 10.497u 0.461s 0:11.26 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 Tue Oct 11 2011 at 06:10:26 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.212095 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): -20.06100 24.02100 ymin,ymax (A): 0.4980000 39.10000 zmin,zma (A): 19.90200 69.77600 x,y,z range (A): 44.08200 38.60200 49.87400 scale (grids/A): 3.212095 object centre (A): 1.980000 19.79900 44.83900 number of atom coordinates read : 2004 total number of charged atoms : 1899 net assigned charge : 7.039010 assigned positive charge : 308.7841 centred at (gu) : 90.49415 94.27746 89.92827 assigned negative charge : -301.7451 centred at (gu) : 89.64280 94.17979 89.81294 start vw surface at 0.7400000 fill in re-entrant regions at 1.390000 boundary points on vw surface= 170342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16990 grid for indexing accessible points = 1.400000 m= 94472 mr = 126236 m= 39501 mr = 78618 m= 11111 mr = 32486 m= 2041 mr = 8463 m= 234 mr = 1427 m= 12 mr = 137 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.560000 number of dielectric boundary points 70335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 3.040000 number of grid points assigned charge 15188 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) : 2.141396 object centre at (A) : 1.980000 19.79900 44.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6835766 0.7450768 midg,1,midg; midg,igrid,midg -7.5768894E-03 0.2769815 1,midg,midg; igrid,midg,midg 0.1545253 0.3570874 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 3.280000 now iterating at: 06:10:30 rms-change max change #iterations 10.29879 404.4354 at 10iterations 6.104232 128.3282 at 20iterations 3.621010 73.32080 at 30iterations 2.138819 41.04331 at 40iterations 1.258619 27.18709 at 50iterations 0.7405681 15.23367 at 60iterations 0.4356677 7.794369 at 70iterations 0.2563250 4.897739 at 80iterations 0.1503733 2.744961 at 90iterations 8.8348821E-02 1.846695 at 100iterations 5.2022088E-02 1.013029 at 110iterations 3.0698864E-02 0.6153412 at 120iterations 1.8307807E-02 0.3324139 at 130iterations 1.1029242E-02 0.2005768 at 140iterations 6.8209828E-03 0.1249542 at 150iterations 4.3723881E-03 8.3084106E-02 at 160iterations 2.9574647E-03 5.1284790E-02 at 170iterations 2.1186355E-03 3.7136078E-02 at 180iterations finished qdiffx linear iterations at : 06:10:46 total time elapsed so far: 19.08000 # loops : 180 mean,max change (kT/e) : 2.1186355E-03 3.7136078E-02 energy calculations done at 19.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.25000 DelPhi exited at 06:10:47 19.251u 0.501s 0:20.05 98.5% 0+0k 0+0io 0pf+0w