Mon Oct 10 17:02:28 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 17:02:29 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7485754 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): 34.54200 82.09900 ymin,ymax (A): 10.95100 52.28600 zmin,zma (A): 25.48700 60.83000 x,y,z range (A): 47.55700 41.33500 35.34300 scale (grids/A): 0.7485754 object centre (A): 58.32050 31.61850 43.15850 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 90.24261 90.31884 88.51047 assigned negative charge : -192.8082 centred at (gu) : 90.38312 90.24942 88.46484 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4857 nv = 96 ne = 84 npr = 27450 no. pairs analyzed = 27450 no. exposed pairs = 1628 no. arc points = 12019 no. surface atoms = 560 nbur = 801 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 406 mr = 2581 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1300000 number of dielectric boundary points 2605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1039 ## 125 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 5181 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9879180E-07 2.8548124E-07 midg,1,midg; midg,igrid,midg 2.7254057E-07 4.1202878E-07 1,midg,midg; igrid,midg,midg 4.2077934E-07 2.4570951E-07 gauss-seidel spectral radius is 0.9906150 estimated iterations to convergence 84 setup time was (sec) 0.3200000 now iterating at: 17:02:29 rms-change max change #iterations 0.1968007 34.88888 at 10iterations 2.6580580E-02 4.592273 at 20iterations 3.6513363E-03 0.6306639 at 30iterations 4.9617240E-04 7.5139999E-02 at 40iterations 6.7580964E-05 1.2966633E-02 at 50iterations finished qdiffx linear iterations at : 17:02:32 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 6.7580964E-05 1.2966633E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 17:02:33 3.361u 0.191s 0:04.31 82.3% 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 17:02:33 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.245726 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): 34.54200 82.09900 ymin,ymax (A): 10.95100 52.28600 zmin,zma (A): 25.48700 60.83000 x,y,z range (A): 47.55700 41.33500 35.34300 scale (grids/A): 2.245726 object centre (A): 58.32050 31.61850 43.15850 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 90.72798 90.95664 85.53140 assigned negative charge : -192.8082 centred at (gu) : 91.14934 90.74829 85.39468 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 50813 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12019 grid for indexing accessible points = 1.400000 m= 19443 mr = 33642 m= 4485 mr = 14375 m= 548 mr = 3056 m= 17 mr = 304 m= 0 mr = 7 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 424 time to turn everything in is 0.2900000 number of dielectric boundary points 23922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 48 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 9868 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) : 0.7485754 object centre at (A) : 58.32050 31.61850 43.15850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4642521E-02 3.1140832E-02 midg,1,midg; midg,igrid,midg 2.9466186E-02 8.7517351E-02 1,midg,midg; igrid,midg,midg 0.1320326 9.9671416E-02 gauss-seidel spectral radius is 0.9988667 estimated iterations to convergence 235 setup time was (sec) 0.4900000 now iterating at: 17:02:34 rms-change max change #iterations 3.967848 223.7319 at 10iterations 1.973199 82.13580 at 20iterations 0.9883354 37.87811 at 30iterations 0.4949478 17.74791 at 40iterations 0.2468986 10.24905 at 50iterations 0.1245664 4.852196 at 60iterations 6.1944976E-02 2.177857 at 70iterations 3.0965090E-02 1.028786 at 80iterations 1.5470724E-02 0.5405293 at 90iterations 7.7284137E-03 0.2790565 at 100iterations 3.8496722E-03 0.1324959 at 110iterations 1.9394187E-03 7.1161270E-02 at 120iterations finished qdiffx linear iterations at : 17:02:41 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.9394187E-03 7.1161270E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 17:02:42 8.066u 0.242s 0:09.21 90.1% 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 17:02:42 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1361 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.368589 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): 34.54200 82.09900 ymin,ymax (A): 10.95100 52.28600 zmin,zma (A): 25.48700 60.83000 x,y,z range (A): 47.55700 41.33500 35.34300 scale (grids/A): 3.368589 object centre (A): 58.32050 31.61850 43.15850 number of atom coordinates read : 1361 total number of charged atoms : 1238 net assigned charge : 16.00000 assigned positive charge : 208.8082 centred at (gu) : 91.09190 91.43492 83.29721 assigned negative charge : -192.8082 centred at (gu) : 91.72398 91.12240 83.09206 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 116860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12019 grid for indexing accessible points = 1.400000 m= 59045 mr = 81138 m= 25541 mr = 47942 m= 8531 mr = 20928 m= 2145 mr = 6673 m= 328 mr = 1630 m= 18 mr = 228 m= 0 mr = 9 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 1525 time to turn everything in is 0.8400000 number of dielectric boundary points 53920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 9904 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) : 2.245726 object centre at (A) : 58.32050 31.61850 43.15850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3659649 0.1669458 midg,1,midg; midg,igrid,midg 0.1438317 0.7204986 1,midg,midg; igrid,midg,midg 1.034977 0.7931635 gauss-seidel spectral radius is 0.9992992 estimated iterations to convergence 298 setup time was (sec) 1.120000 now iterating at: 17:02:44 rms-change max change #iterations 8.649939 365.9163 at 10iterations 5.065642 118.3980 at 20iterations 2.963195 78.67084 at 30iterations 1.731546 36.20467 at 40iterations 1.010892 26.80349 at 50iterations 0.5900846 12.08200 at 60iterations 0.3437407 6.642750 at 70iterations 0.2002363 3.956370 at 80iterations 0.1165323 2.357716 at 90iterations 6.7983285E-02 1.367336 at 100iterations 3.9538153E-02 0.7938232 at 110iterations 2.2956220E-02 0.4918671 at 120iterations 1.3404577E-02 0.2630696 at 130iterations 7.8184642E-03 0.1642914 at 140iterations 4.5507462E-03 8.6679459E-02 at 150iterations 2.6462558E-03 5.3688049E-02 at 160iterations 1.5413400E-03 3.5245895E-02 at 170iterations 8.9569011E-04 1.8165588E-02 at 180iterations finished qdiffx linear iterations at : 17:02:56 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 8.9569011E-04 1.8165588E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 17:02:57 13.168u 0.296s 0:14.27 94.2% 0+0k 0+0io 0pf+0w