Mon Oct 10 01:19:53 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 Mon Oct 10 2011 at 01:19:53 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6396780 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): -6.079000 34.89100 ymin,ymax (A): -3.641000 48.38000 zmin,zma (A): -24.40600 31.24700 x,y,z range (A): 40.97000 52.02100 55.65300 scale (grids/A): 0.6396780 object centre (A): 14.40600 22.36950 3.420500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.89458 92.60027 90.17520 assigned negative charge : -288.8262 centred at (gu) : 91.01732 92.73237 90.13136 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5473 nv = 96 ne = 84 npr = 40427 no. pairs analyzed = 40427 no. exposed pairs = 2474 no. arc points = 17570 no. surface atoms = 840 nbur = 1124 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3033 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.1600000 number of dielectric boundary points 2705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5185571E-10 8.7741867E-09 midg,1,midg; midg,igrid,midg 9.1309547E-09 -1.2157289E-08 1,midg,midg; igrid,midg,midg 1.2436081E-08 -7.1971904E-09 gauss-seidel spectral radius is 0.9872831 estimated iterations to convergence 72 setup time was (sec) 0.3500000 now iterating at: 01:19:53 rms-change max change #iterations 0.1266758 17.87833 at 10iterations 1.2365000E-02 1.883301 at 20iterations 1.2538788E-03 0.1771164 at 30iterations 1.2105775E-04 1.8695831E-02 at 40iterations 1.1990696E-05 1.9283295E-03 at 50iterations finished qdiffx linear iterations at : 01:19:56 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 1.1990696E-05 1.9283295E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 01:19:57 3.297u 0.166s 0:03.85 89.6% 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 01:19:57 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.919034 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): -6.079000 34.89100 ymin,ymax (A): -3.641000 48.38000 zmin,zma (A): -24.40600 31.24700 x,y,z range (A): 40.97000 52.02100 55.65300 scale (grids/A): 1.919034 object centre (A): 14.40600 22.36950 3.420500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 92.68377 97.80077 90.52547 assigned negative charge : -288.8262 centred at (gu) : 93.05198 98.19732 90.39418 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 58898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17570 grid for indexing accessible points = 1.400000 m= 21944 mr = 40311 m= 3485 mr = 16806 m= 164 mr = 2324 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1490 time to turn everything in is 0.2900000 number of dielectric boundary points 24986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 14437 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) : 0.6396780 object centre at (A) : 14.40600 22.36950 3.420500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7757190E-02 1.3627022E-02 midg,1,midg; midg,igrid,midg 3.6250036E-02 -8.6131291E-03 1,midg,midg; igrid,midg,midg 9.0345778E-03 -6.2286640E-03 gauss-seidel spectral radius is 0.9985773 estimated iterations to convergence 210 setup time was (sec) 0.5000000 now iterating at: 01:19:57 rms-change max change #iterations 3.652701 194.2406 at 10iterations 1.682173 63.40569 at 20iterations 0.7799128 31.73770 at 30iterations 0.3582188 12.90098 at 40iterations 0.1648697 6.291924 at 50iterations 7.6173268E-02 2.593014 at 60iterations 3.4871683E-02 1.206631 at 70iterations 1.6053753E-02 0.5422363 at 80iterations 7.4248975E-03 0.2602222 at 90iterations 3.4286720E-03 0.1276550 at 100iterations 1.5794042E-03 5.1552296E-02 at 110iterations 7.2629628E-04 2.7770996E-02 at 120iterations finished qdiffx linear iterations at : 01:20:04 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 7.2629628E-04 2.7770996E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 01:20:05 7.526u 0.203s 0:08.00 96.5% 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 01:20:05 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878551 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): -6.079000 34.89100 ymin,ymax (A): -3.641000 48.38000 zmin,zma (A): -24.40600 31.24700 x,y,z range (A): 40.97000 52.02100 55.65300 scale (grids/A): 2.878551 object centre (A): 14.40600 22.36950 3.420500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 94.02567 101.7012 90.78819 assigned negative charge : -288.8262 centred at (gu) : 94.57802 102.2959 90.59129 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 135732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17570 grid for indexing accessible points = 1.400000 m= 69713 mr = 97459 m= 26705 mr = 57669 m= 6184 mr = 22260 m= 710 mr = 4880 m= 42 mr = 485 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 4962 time to turn everything in is 0.7600000 number of dielectric boundary points 56308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 14656 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) : 1.919034 object centre at (A) : 14.40600 22.36950 3.420500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.080938 2.1176444E-02 midg,1,midg; midg,igrid,midg 0.3566857 -0.1017407 1,midg,midg; igrid,midg,midg 5.8382370E-02 -3.9665133E-02 gauss-seidel spectral radius is 0.9992306 estimated iterations to convergence 285 setup time was (sec) 0.9800000 now iterating at: 01:20:06 rms-change max change #iterations 8.595172 432.2754 at 10iterations 4.927443 112.4455 at 20iterations 2.796406 61.23764 at 30iterations 1.589125 37.19964 at 40iterations 0.9003848 19.35448 at 50iterations 0.5099941 10.81295 at 60iterations 0.2889782 5.635420 at 70iterations 0.1639720 3.452625 at 80iterations 9.3119636E-02 1.846238 at 90iterations 5.2685037E-02 1.030666 at 100iterations 2.9793538E-02 0.6568756 at 110iterations 1.6910415E-02 0.3489828 at 120iterations 9.5928740E-03 0.2026787 at 130iterations 5.4250532E-03 0.1176023 at 140iterations 3.0788102E-03 6.1516762E-02 at 150iterations 1.7492927E-03 3.4313202E-02 at 160iterations 9.8931207E-04 1.9348145E-02 at 170iterations 5.6202448E-04 1.1741638E-02 at 180iterations finished qdiffx linear iterations at : 01:20:17 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 5.6202448E-04 1.1741638E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 01:20:17 11.978u 0.197s 0:12.52 97.1% 0+0k 0+0io 0pf+0w