Sun Oct 9 15:51:50 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 15:51:50 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 = 5617 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5057177 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): 33.52600 103.9210 ymin,ymax (A): -5.945000 57.53000 zmin,zma (A): -32.64700 34.70900 x,y,z range (A): 70.39500 63.47500 67.35600 scale (grids/A): 0.5057177 object centre (A): 68.72350 25.79250 1.031000 number of atom coordinates read : 5617 total number of charged atoms : 5446 net assigned charge : -3.499954 assigned positive charge : 857.1073 centred at (gu) : 90.05551 90.75662 89.36500 assigned negative charge : -860.6150 centred at (gu) : 89.98926 90.68805 89.25038 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8912 nv = 96 ne = 84 npr = 115753 no. pairs analyzed = 115753 no. exposed pairs = 6391 no. arc points = 44441 no. surface atoms = 2140 nbur = 3477 mkacc time = 0.2000000 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 = 1.680000 m= 305 mr = 4985 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3700000 number of dielectric boundary points 4218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4239 ## 638 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 12024 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9617776E-10 2.0760277E-10 midg,1,midg; midg,igrid,midg -1.7515017E-10 1.6352930E-10 1,midg,midg; igrid,midg,midg -2.0526832E-10 1.2902047E-10 gauss-seidel spectral radius is 0.9800542 estimated iterations to convergence 59 setup time was (sec) 0.5600000 now iterating at: 15:51:51 rms-change max change #iterations 7.0979550E-02 12.54527 at 10iterations 4.4012740E-03 0.6167068 at 20iterations 5.2767282E-04 8.1501007E-02 at 30iterations 1.1982344E-04 1.7190933E-02 at 40iterations 3.3710141E-05 4.3888092E-03 at 50iterations finished qdiffx linear iterations at : 15:51:53 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 3.3710141E-05 4.3888092E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:51:54 3.613u 0.193s 0:04.15 91.5% 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 Sun Oct 9 2011 at 15:51:54 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 = 5617 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.517153 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): 33.52600 103.9210 ymin,ymax (A): -5.945000 57.53000 zmin,zma (A): -32.64700 34.70900 x,y,z range (A): 70.39500 63.47500 67.35600 scale (grids/A): 1.517153 object centre (A): 68.72350 25.79250 1.031000 number of atom coordinates read : 5617 total number of charged atoms : 5446 net assigned charge : -3.499954 assigned positive charge : 857.1073 centred at (gu) : 90.16503 92.26820 88.09332 assigned negative charge : -860.6150 centred at (gu) : 89.96774 92.06403 87.75079 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 101791 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44441 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30326 mr = 72695 m= 2732 mr = 21124 m= 55 mr = 1210 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4852 time to turn everything in is 0.5100000 number of dielectric boundary points 39875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 575 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 40707 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) : 0.5057177 object centre at (A) : 68.72350 25.79250 1.031000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1792850E-02 5.0898483E-03 midg,1,midg; midg,igrid,midg -1.0433622E-02 6.9967923E-03 1,midg,midg; igrid,midg,midg -1.1545327E-02 -1.9583557E-02 gauss-seidel spectral radius is 0.9981351 estimated iterations to convergence 184 setup time was (sec) 0.7300000 now iterating at: 15:51:55 rms-change max change #iterations 4.120262 154.1792 at 10iterations 1.693331 57.59469 at 20iterations 0.6988420 21.72920 at 30iterations 0.2881083 8.973484 at 40iterations 0.1193900 3.565440 at 50iterations 4.9284820E-02 1.507504 at 60iterations 2.0373832E-02 0.6332436 at 70iterations 8.4458850E-03 0.2398056 at 80iterations 3.5199157E-03 0.1018534 at 90iterations 1.4714601E-03 4.3548584E-02 at 100iterations 6.2228070E-04 1.8333435E-02 at 110iterations 2.7280199E-04 8.1691742E-03 at 120iterations finished qdiffx linear iterations at : 15:52:02 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 2.7280199E-04 8.1691742E-03 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 15:52:03 8.076u 0.188s 0:08.61 95.8% 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 15:52:03 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 = 5617 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.275730 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): 33.52600 103.9210 ymin,ymax (A): -5.945000 57.53000 zmin,zma (A): -32.64700 34.70900 x,y,z range (A): 70.39500 63.47500 67.35600 scale (grids/A): 2.275730 object centre (A): 68.72350 25.79250 1.031000 number of atom coordinates read : 5617 total number of charged atoms : 5446 net assigned charge : -3.499954 assigned positive charge : 857.1073 centred at (gu) : 90.24699 93.40189 87.13967 assigned negative charge : -860.6150 centred at (gu) : 89.95147 93.09601 86.62626 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 237982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44441 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 108518 mr = 178279 m= 28305 mr = 86889 m= 4101 mr = 21251 m= 238 mr = 2566 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 16288 time to turn everything in is 1.200000 number of dielectric boundary points 90102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 43424 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) : 1.517153 object centre at (A) : 68.72350 25.79250 1.031000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1622101 4.2231236E-02 midg,1,midg; midg,igrid,midg -0.2198737 0.1997103 1,midg,midg; igrid,midg,midg -0.1089953 -0.5635334 gauss-seidel spectral radius is 0.9991780 estimated iterations to convergence 275 setup time was (sec) 1.450000 now iterating at: 15:52:04 rms-change max change #iterations 11.07108 297.6688 at 10iterations 6.325030 141.9905 at 20iterations 3.597655 75.95990 at 30iterations 2.036607 43.21205 at 40iterations 1.149107 22.44848 at 50iterations 0.6463413 13.30028 at 60iterations 0.3628066 7.846318 at 70iterations 0.2036012 3.734764 at 80iterations 0.1140937 2.136965 at 90iterations 6.3827254E-02 1.110157 at 100iterations 3.5754181E-02 0.6057129 at 110iterations 1.9984541E-02 0.3283424 at 120iterations 1.1152600E-02 0.2070656 at 130iterations 6.2307511E-03 0.1215839 at 140iterations 3.4844230E-03 6.0765490E-02 at 150iterations 1.9478083E-03 3.3611298E-02 at 160iterations 1.0925630E-03 2.0919800E-02 at 170iterations 6.1073730E-04 1.0498762E-02 at 180iterations finished qdiffx linear iterations at : 15:52:16 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 6.1073730E-04 1.0498762E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 15:52:16 13.232u 0.203s 0:13.77 97.5% 0+0k 0+0io 0pf+0w