Sun Oct 9 15:28:10 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+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 Sun Oct 9 2011 at 15:28:10 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 = 5500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5136862 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): 25.17100 86.12000 ymin,ymax (A): 11.29500 80.59800 zmin,zma (A): -30.96500 33.60800 x,y,z range (A): 60.94900 69.30300 64.57300 scale (grids/A): 0.5136862 object centre (A): 55.64550 45.94650 1.321499 number of atom coordinates read : 5500 total number of charged atoms : 5329 net assigned charge : -5.999956 assigned positive charge : 842.4719 centred at (gu) : 91.11326 90.16991 89.44095 assigned negative charge : -848.4790 centred at (gu) : 91.04564 90.09934 89.51502 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8822 nv = 96 ne = 84 npr = 114858 no. pairs analyzed = 114858 no. exposed pairs = 6226 no. arc points = 42499 no. surface atoms = 2097 nbur = 3403 mkacc time = 0.2400000 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 = 1.652000 m= 277 mr = 4878 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.5100000 number of dielectric boundary points 4214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4176 ## 576 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8082015E-10 -3.1528452E-10 midg,1,midg; midg,igrid,midg -3.3711972E-10 1.4984587E-10 1,midg,midg; igrid,midg,midg -2.5569055E-10 1.8076289E-10 gauss-seidel spectral radius is 0.9806543 estimated iterations to convergence 59 setup time was (sec) 0.7300000 now iterating at: 15:28:11 rms-change max change #iterations 7.6594986E-02 10.50208 at 10iterations 5.1781740E-03 0.8492088 at 20iterations 7.6998555E-04 0.1113415 at 30iterations 2.0180512E-04 2.8955460E-02 at 40iterations 5.5405384E-05 7.6904297E-03 at 50iterations finished qdiffx linear iterations at : 15:28:13 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 5.5405384E-05 7.6904297E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 15:28:14 3.512u 0.149s 0:03.93 92.8% 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 15:28:14 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 = 5500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.541059 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): 25.17100 86.12000 ymin,ymax (A): 11.29500 80.59800 zmin,zma (A): -30.96500 33.60800 x,y,z range (A): 60.94900 69.30300 64.57300 scale (grids/A): 1.541059 object centre (A): 55.64550 45.94650 1.321499 number of atom coordinates read : 5500 total number of charged atoms : 5329 net assigned charge : -5.999956 assigned positive charge : 842.4719 centred at (gu) : 93.33862 90.50867 88.32088 assigned negative charge : -848.4790 centred at (gu) : 93.13642 90.29760 88.54499 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 100295 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 29438 mr = 71369 m= 2593 mr = 20481 m= 46 mr = 1244 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3483 time to turn everything in is 0.6500000 number of dielectric boundary points 39278 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 490 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 40095 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) : 0.5136862 object centre at (A) : 55.64550 45.94650 1.321499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7534002E-03 4.4528283E-03 midg,1,midg; midg,igrid,midg -1.6936995E-02 -1.9549321E-02 1,midg,midg; igrid,midg,midg -1.1652092E-02 1.2785736E-02 gauss-seidel spectral radius is 0.9981812 estimated iterations to convergence 186 setup time was (sec) 0.9200000 now iterating at: 15:28:15 rms-change max change #iterations 4.241861 157.3429 at 10iterations 1.772296 53.94831 at 20iterations 0.7395356 22.86866 at 30iterations 0.3088049 8.977886 at 40iterations 0.1290594 3.980347 at 50iterations 5.3950626E-02 1.681892 at 60iterations 2.2683531E-02 0.7061577 at 70iterations 9.4949678E-03 0.2758141 at 80iterations 4.0038214E-03 0.1215744 at 90iterations 1.7010083E-03 5.3087234E-02 at 100iterations 7.3769549E-04 2.3474693E-02 at 110iterations 3.2735121E-04 9.7961426E-03 at 120iterations finished qdiffx linear iterations at : 15:28:21 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 3.2735121E-04 9.7961426E-03 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 15:28:21 7.200u 0.181s 0:07.66 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 15:28:22 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 = 5500 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.311588 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): 25.17100 86.12000 ymin,ymax (A): 11.29500 80.59800 zmin,zma (A): -30.96500 33.60800 x,y,z range (A): 60.94900 69.30300 64.57300 scale (grids/A): 2.311588 object centre (A): 55.64550 45.94650 1.321499 number of atom coordinates read : 5500 total number of charged atoms : 5329 net assigned charge : -5.999956 assigned positive charge : 842.4719 centred at (gu) : 95.00722 90.76247 87.48093 assigned negative charge : -848.4790 centred at (gu) : 94.70480 90.44640 87.81739 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 234333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42499 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 105475 mr = 175155 m= 27218 mr = 84184 m= 3751 mr = 20524 m= 206 mr = 2407 m= 2 mr = 69 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 11648 time to turn everything in is 1.600000 number of dielectric boundary points 88647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 42543 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) : 1.541059 object centre at (A) : 55.64550 45.94650 1.321499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1535518 0.2956858 midg,1,midg; midg,igrid,midg -0.2703318 -0.5803281 1,midg,midg; igrid,midg,midg -0.1593405 0.3298581 gauss-seidel spectral radius is 0.9991913 estimated iterations to convergence 278 setup time was (sec) 1.890000 now iterating at: 15:28:24 rms-change max change #iterations 11.29991 269.9095 at 10iterations 6.502258 138.8947 at 20iterations 3.709766 81.17635 at 30iterations 2.109732 45.65686 at 40iterations 1.195361 25.65365 at 50iterations 0.6774418 16.45349 at 60iterations 0.3819670 7.544239 at 70iterations 0.2157229 3.699749 at 80iterations 0.1211624 2.170746 at 90iterations 6.8236932E-02 1.221687 at 100iterations 3.8388111E-02 0.6623878 at 110iterations 2.1563958E-02 0.3680687 at 120iterations 1.2121433E-02 0.2241879 at 130iterations 6.8032751E-03 0.1196642 at 140iterations 3.8206440E-03 6.7111969E-02 at 150iterations 2.1502462E-03 3.8999557E-02 at 160iterations 1.2096786E-03 2.4208069E-02 at 170iterations 6.7986286E-04 1.1232376E-02 at 180iterations finished qdiffx linear iterations at : 15:28:33 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 6.7986286E-04 1.1232376E-02 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 15:28:34 11.662u 0.174s 0:12.11 97.6% 0+0k 0+0io 0pf+0w