Mon Oct 10 17:04:43 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 17:04:43 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1788 !!! WARNING: HIT 148 has a net charge of 0.5140 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: 0.7059150 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): -26.67100 20.80500 ymin,ymax (A): -1.401000 38.22100 zmin,zma (A): 25.12600 75.55700 x,y,z range (A): 47.47600 39.62200 50.43100 scale (grids/A): 0.7059150 object centre (A): -2.933000 18.41000 50.34150 number of atom coordinates read : 1788 total number of charged atoms : 1659 net assigned charge : -4.485982 assigned positive charge : 260.4094 centred at (gu) : 88.51340 89.96371 91.27512 assigned negative charge : -264.8951 centred at (gu) : 88.59975 90.07225 91.33968 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6125 nv = 96 ne = 84 npr = 37585 no. pairs analyzed = 37585 no. exposed pairs = 2230 no. arc points = 16445 no. surface atoms = 765 nbur = 1023 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3265 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.2800000 number of dielectric boundary points 3160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1368 ## 109 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6641663E-09 -8.0521112E-08 midg,1,midg; midg,igrid,midg 6.9314807E-09 -8.0335852E-08 1,midg,midg; igrid,midg,midg -1.7466593E-09 -5.3905715E-08 gauss-seidel spectral radius is 0.9895229 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 17:04:44 rms-change max change #iterations 0.1905316 28.63644 at 10iterations 2.2912160E-02 3.380867 at 20iterations 2.8225393E-03 0.4316578 at 30iterations 3.4280849E-04 5.1923752E-02 at 40iterations 4.2286498E-05 6.6356659E-03 at 50iterations finished qdiffx linear iterations at : 17:04:48 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 4.2286498E-05 6.6356659E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 17:04:48 4.085u 0.255s 0:04.78 90.5% 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 17:04:48 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1788 !!! WARNING: HIT 148 has a net charge of 0.5140 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: 2.117745 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): -26.67100 20.80500 ymin,ymax (A): -1.401000 38.22100 zmin,zma (A): 25.12600 75.55700 x,y,z range (A): 47.47600 39.62200 50.43100 scale (grids/A): 2.117745 object centre (A): -2.933000 18.41000 50.34150 number of atom coordinates read : 1788 total number of charged atoms : 1659 net assigned charge : -4.485982 assigned positive charge : 260.4094 centred at (gu) : 85.54036 89.89137 93.82559 assigned negative charge : -264.8951 centred at (gu) : 85.79932 90.21687 94.01907 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16445 grid for indexing accessible points = 1.400000 m= 22921 mr = 43517 m= 4061 mr = 16795 m= 339 mr = 2669 m= 8 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 579 time to turn everything in is 0.5900000 number of dielectric boundary points 28965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13170 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) : 0.7059150 object centre at (A) : -2.933000 18.41000 50.34150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9390939E-02 -7.6178700E-02 midg,1,midg; midg,igrid,midg 1.6973609E-02 -1.8847061E-02 1,midg,midg; igrid,midg,midg 3.4239408E-02 2.1769868E-02 gauss-seidel spectral radius is 0.9988132 estimated iterations to convergence 230 setup time was (sec) 0.9100000 now iterating at: 17:04:49 rms-change max change #iterations 4.253373 189.3904 at 10iterations 2.084760 78.77570 at 20iterations 1.022159 36.17276 at 30iterations 0.5039262 17.59533 at 40iterations 0.2474684 7.996400 at 50iterations 0.1221311 3.815202 at 60iterations 6.0186725E-02 1.938811 at 70iterations 2.9481877E-02 0.9275723 at 80iterations 1.4547637E-02 0.4436064 at 90iterations 7.1908538E-03 0.2346420 at 100iterations 3.5246643E-03 0.1199648 at 110iterations 1.7350751E-03 5.7518005E-02 at 120iterations finished qdiffx linear iterations at : 17:04:58 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 1.7350751E-03 5.7518005E-02 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 17:04:59 9.474u 0.300s 0:10.30 94.8% 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 Mon Oct 10 2011 at 17:04:59 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1788 !!! WARNING: HIT 148 has a net charge of 0.5140 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: 3.176618 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): -26.67100 20.80500 ymin,ymax (A): -1.401000 38.22100 zmin,zma (A): 25.12600 75.55700 x,y,z range (A): 47.47600 39.62200 50.43100 scale (grids/A): 3.176618 object centre (A): -2.933000 18.41000 50.34150 number of atom coordinates read : 1788 total number of charged atoms : 1659 net assigned charge : -4.485982 assigned positive charge : 260.4094 centred at (gu) : 83.31058 89.83709 95.73860 assigned negative charge : -264.8951 centred at (gu) : 83.69904 90.32537 96.02862 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 149408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16445 grid for indexing accessible points = 1.400000 m= 73232 mr = 105369 m= 27657 mr = 59451 m= 7573 mr = 22345 m= 1419 mr = 5801 m= 144 mr = 1002 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 1872 time to turn everything in is 1.870000 number of dielectric boundary points 65377 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 13272 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) : 2.117745 object centre at (A) : -2.933000 18.41000 50.34150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9880501 -0.6838780 midg,1,midg; midg,igrid,midg 0.1256181 -0.1409735 1,midg,midg; igrid,midg,midg 0.2697120 0.2840385 gauss-seidel spectral radius is 0.9992964 estimated iterations to convergence 297 setup time was (sec) 2.200000 now iterating at: 17:05:01 rms-change max change #iterations 9.489545 382.3712 at 10iterations 5.553756 131.3840 at 20iterations 3.252519 70.42561 at 30iterations 1.901583 40.41495 at 40iterations 1.108218 21.50284 at 50iterations 0.6485242 12.41671 at 60iterations 0.3775771 7.490247 at 70iterations 0.2203445 4.276121 at 80iterations 0.1279974 2.496475 at 90iterations 7.4460641E-02 1.479005 at 100iterations 4.3376144E-02 0.9128246 at 110iterations 2.5262857E-02 0.4698753 at 120iterations 1.4734562E-02 0.2808743 at 130iterations 8.5623274E-03 0.1563635 at 140iterations 4.9857413E-03 9.7156525E-02 at 150iterations 2.9094692E-03 5.2935600E-02 at 160iterations 1.6931848E-03 3.1379700E-02 at 170iterations 9.8719052E-04 2.1309853E-02 at 180iterations finished qdiffx linear iterations at : 17:05:15 total time elapsed so far: 15.89000 # loops : 180 mean,max change (kT/e) : 9.8719052E-04 2.1309853E-02 energy calculations done at 15.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.07000 DelPhi exited at 17:05:15 16.067u 0.322s 0:16.83 97.3% 0+0k 0+0io 0pf+0w