Mon Oct 10 00:49:15 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 Mon Oct 10 2011 at 00:49:15 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 = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6325740 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): -9.443000 38.82900 ymin,ymax (A): -53.81600 -4.067000 zmin,zma (A): -20.63800 35.64000 x,y,z range (A): 48.27200 49.74900 56.27800 scale (grids/A): 0.6325740 object centre (A): 14.69300 -28.94150 7.501001 number of atom coordinates read : 2594 total number of charged atoms : 2451 net assigned charge : 2.000015 assigned positive charge : 390.9850 centred at (gu) : 90.36008 89.77064 89.74870 assigned negative charge : -388.9857 centred at (gu) : 90.35926 89.78548 89.73747 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7041 nv = 96 ne = 84 npr = 51791 no. pairs analyzed = 51791 no. exposed pairs = 3491 no. arc points = 24261 no. surface atoms = 1187 nbur = 1407 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3713 m= 0 mr = 34 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2308 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3399223E-09 3.2369549E-09 midg,1,midg; midg,igrid,midg 3.9465800E-09 8.8927171E-10 1,midg,midg; igrid,midg,midg 2.1045470E-09 2.6136073E-09 gauss-seidel spectral radius is 0.9870611 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 00:49:16 rms-change max change #iterations 0.1396596 23.25597 at 10iterations 1.3413076E-02 2.082783 at 20iterations 1.3120702E-03 0.2082481 at 30iterations 1.2633983E-04 1.8363953E-02 at 40iterations 1.4114945E-05 1.8692017E-03 at 50iterations finished qdiffx linear iterations at : 00:49:19 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.4114945E-05 1.8692017E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 00:49:19 3.606u 0.176s 0:04.10 91.9% 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 Mon Oct 10 2011 at 00:49:19 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 = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.897722 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): -9.443000 38.82900 ymin,ymax (A): -53.81600 -4.067000 zmin,zma (A): -20.63800 35.64000 x,y,z range (A): 48.27200 49.74900 56.27800 scale (grids/A): 1.897722 object centre (A): 14.69300 -28.94150 7.501001 number of atom coordinates read : 2594 total number of charged atoms : 2451 net assigned charge : 2.000015 assigned positive charge : 390.9850 centred at (gu) : 91.07979 89.31139 89.24544 assigned negative charge : -388.9857 centred at (gu) : 91.07741 89.35648 89.21231 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 76054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24261 grid for indexing accessible points = 1.400000 m= 26660 mr = 51312 m= 4380 mr = 19107 m= 293 mr = 2778 m= 0 mr = 96 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.6000000 number of dielectric boundary points 34094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19296 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) : 0.6325740 object centre at (A) : 14.69300 -28.94150 7.501001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9010529E-02 5.1577747E-02 midg,1,midg; midg,igrid,midg -5.2049197E-04 -1.9879175E-02 1,midg,midg; igrid,midg,midg 1.2359355E-02 -6.3100657E-03 gauss-seidel spectral radius is 0.9986418 estimated iterations to convergence 215 setup time was (sec) 0.9000000 now iterating at: 00:49:20 rms-change max change #iterations 4.252321 164.6602 at 10iterations 2.000643 71.63322 at 20iterations 0.9457005 30.87348 at 30iterations 0.4432874 15.88721 at 40iterations 0.2078303 7.291956 at 50iterations 9.8106682E-02 3.086346 at 60iterations 4.6040561E-02 1.479307 at 70iterations 2.1612028E-02 0.6264391 at 80iterations 1.0148538E-02 0.3334999 at 90iterations 4.7787814E-03 0.1531200 at 100iterations 2.2408396E-03 7.1066856E-02 at 110iterations 1.0551937E-03 3.4950256E-02 at 120iterations finished qdiffx linear iterations at : 00:49:27 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.0551937E-03 3.4950256E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 00:49:27 7.680u 0.199s 0:08.25 95.3% 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 Mon Oct 10 2011 at 00:49:28 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 = 2594 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.846583 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): -9.443000 38.82900 ymin,ymax (A): -53.81600 -4.067000 zmin,zma (A): -20.63800 35.64000 x,y,z range (A): 48.27200 49.74900 56.27800 scale (grids/A): 2.846583 object centre (A): 14.69300 -28.94150 7.501001 number of atom coordinates read : 2594 total number of charged atoms : 2451 net assigned charge : 2.000015 assigned positive charge : 390.9850 centred at (gu) : 91.61949 88.96696 88.86810 assigned negative charge : -388.9857 centred at (gu) : 91.61618 89.03472 88.81843 start vw surface at 0.1800000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 175836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24261 grid for indexing accessible points = 1.400000 m= 85918 mr = 124974 m= 31250 mr = 68794 m= 8035 mr = 24750 m= 1286 mr = 6088 m= 82 mr = 867 m= 0 mr = 29 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 181 time to turn everything in is 1.470000 number of dielectric boundary points 76905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 19608 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) : 1.897722 object centre at (A) : 14.69300 -28.94150 7.501001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2277679 0.9936033 midg,1,midg; midg,igrid,midg -1.1815645E-03 -0.2703141 1,midg,midg; igrid,midg,midg 0.2350538 -6.3044623E-02 gauss-seidel spectral radius is 0.9992699 estimated iterations to convergence 292 setup time was (sec) 1.780000 now iterating at: 00:49:29 rms-change max change #iterations 10.07719 350.4929 at 10iterations 5.996769 128.6220 at 20iterations 3.533342 87.03299 at 30iterations 2.071820 42.00771 at 40iterations 1.212558 25.40232 at 50iterations 0.7040930 14.48644 at 60iterations 0.4094132 7.392227 at 70iterations 0.2368363 4.391015 at 80iterations 0.1373006 2.540833 at 90iterations 7.9235420E-02 1.350670 at 100iterations 4.5819197E-02 0.8612003 at 110iterations 2.6497968E-02 0.4882603 at 120iterations 1.5296446E-02 0.2823315 at 130iterations 8.8290907E-03 0.1636505 at 140iterations 5.0924704E-03 9.1415405E-02 at 150iterations 2.9328377E-03 5.7238579E-02 at 160iterations 1.6944316E-03 3.0218124E-02 at 170iterations 9.7733550E-04 1.7228305E-02 at 180iterations finished qdiffx linear iterations at : 00:49:40 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 9.7733550E-04 1.7228305E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 00:49:40 12.039u 0.198s 0:12.52 97.6% 0+0k 0+0io 0pf+0w