Tue Oct 11 06:53:34 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 Tue Oct 11 2011 at 06:53:34 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 = 2501 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: 0.6442389 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): -10.65100 44.60800 ymin,ymax (A): 24.43500 79.58300 zmin,zma (A): -70.84200 -27.56500 x,y,z range (A): 55.25900 55.14800 43.27700 scale (grids/A): 0.6442389 object centre (A): 16.97850 52.00900 -49.20350 number of atom coordinates read : 2501 total number of charged atoms : 2363 net assigned charge : -2.499992 assigned positive charge : 358.4951 centred at (gu) : 88.85719 90.14291 89.86203 assigned negative charge : -360.9956 centred at (gu) : 88.95087 90.32938 89.85882 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7201 nv = 96 ne = 84 npr = 50533 no. pairs analyzed = 50533 no. exposed pairs = 3364 no. arc points = 23959 no. surface atoms = 1134 nbur = 1367 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 432 mr = 3769 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 179 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8367 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7065227E-09 -3.6877497E-09 midg,1,midg; midg,igrid,midg 1.7481385E-08 -2.8177961E-08 1,midg,midg; igrid,midg,midg 9.1769889E-09 -1.2308663E-08 gauss-seidel spectral radius is 0.9875191 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 06:53:35 rms-change max change #iterations 0.1453930 24.82096 at 10iterations 1.4624044E-02 2.267666 at 20iterations 1.4496554E-03 0.2027016 at 30iterations 1.4839688E-04 2.4169922E-02 at 40iterations 1.6258113E-05 2.4642944E-03 at 50iterations finished qdiffx linear iterations at : 06:53:37 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.6258113E-05 2.4642944E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:53:38 3.358u 0.166s 0:04.13 84.9% 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 Tue Oct 11 2011 at 06:53:38 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 = 2501 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: 1.932717 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): -10.65100 44.60800 ymin,ymax (A): 24.43500 79.58300 zmin,zma (A): -70.84200 -27.56500 x,y,z range (A): 55.25900 55.14800 43.27700 scale (grids/A): 1.932717 object centre (A): 16.97850 52.00900 -49.20350 number of atom coordinates read : 2501 total number of charged atoms : 2363 net assigned charge : -2.499992 assigned positive charge : 358.4951 centred at (gu) : 86.57099 90.42830 89.58562 assigned negative charge : -360.9956 centred at (gu) : 86.85249 90.98805 89.57620 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23959 grid for indexing accessible points = 1.400000 m= 29156 mr = 51609 m= 5202 mr = 21345 m= 325 mr = 3249 m= 6 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 35130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18636 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) : 0.6442389 object centre at (A) : 16.97850 52.00900 -49.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2543472E-02 1.4671576E-02 midg,1,midg; midg,igrid,midg -8.6492728E-03 -4.9269576E-02 1,midg,midg; igrid,midg,midg -1.2316529E-03 -5.4085623E-02 gauss-seidel spectral radius is 0.9986787 estimated iterations to convergence 218 setup time was (sec) 0.5900000 now iterating at: 06:53:39 rms-change max change #iterations 4.185268 202.7350 at 10iterations 1.990880 65.20579 at 20iterations 0.9446185 30.95173 at 30iterations 0.4488738 14.68106 at 40iterations 0.2126651 6.938788 at 50iterations 0.1011261 3.768749 at 60iterations 4.7952715E-02 1.523651 at 70iterations 2.2750046E-02 0.7642193 at 80iterations 1.0812190E-02 0.3489532 at 90iterations 5.1265941E-03 0.1698132 at 100iterations 2.4291165E-03 8.2032204E-02 at 110iterations 1.1526711E-03 3.3950806E-02 at 120iterations finished qdiffx linear iterations at : 06:53:46 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.1526711E-03 3.3950806E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 06:53:46 7.769u 0.205s 0:08.27 96.2% 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 06:53:47 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 = 2501 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: 2.899075 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): -10.65100 44.60800 ymin,ymax (A): 24.43500 79.58300 zmin,zma (A): -70.84200 -27.56500 x,y,z range (A): 55.25900 55.14800 43.27700 scale (grids/A): 2.899075 object centre (A): 16.97850 52.00900 -49.20350 number of atom coordinates read : 2501 total number of charged atoms : 2363 net assigned charge : -2.499992 assigned positive charge : 358.4951 centred at (gu) : 84.85649 90.64248 89.37823 assigned negative charge : -360.9956 centred at (gu) : 85.27867 91.48209 89.36429 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 176898 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23959 grid for indexing accessible points = 1.400000 m= 90868 mr = 125133 m= 36233 mr = 73521 m= 9344 mr = 29162 m= 1351 mr = 6906 m= 91 mr = 867 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 79173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18898 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) : 1.932717 object centre at (A) : 16.97850 52.00900 -49.20350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1701611 0.2089074 midg,1,midg; midg,igrid,midg -4.6957735E-02 -0.2263238 1,midg,midg; igrid,midg,midg -4.3848880E-02 -1.015897 gauss-seidel spectral radius is 0.9992902 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 06:53:48 rms-change max change #iterations 9.859500 396.3812 at 10iterations 5.893082 127.5381 at 20iterations 3.487868 74.93891 at 30iterations 2.053959 44.79169 at 40iterations 1.211064 23.94548 at 50iterations 0.7089858 13.52739 at 60iterations 0.4151273 8.942453 at 70iterations 0.2424058 4.393799 at 80iterations 0.1415711 2.624761 at 90iterations 8.2614549E-02 1.572954 at 100iterations 4.8075993E-02 0.8333921 at 110iterations 2.7991872E-02 0.5221586 at 120iterations 1.6285960E-02 0.2861136 at 130iterations 9.5191123E-03 0.1605120 at 140iterations 5.5304947E-03 9.9151373E-02 at 150iterations 3.2111462E-03 6.8470001E-02 at 160iterations 1.8707289E-03 3.6319733E-02 at 170iterations 1.0891310E-03 2.0492554E-02 at 180iterations finished qdiffx linear iterations at : 06:54:01 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 1.0891310E-03 2.0492554E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.09000 DelPhi exited at 06:54:01 14.091u 0.211s 0:14.57 98.1% 0+0k 0+0io 0pf+0w