Sat Oct 8 17:26:18 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 Sat Oct 8 2011 at 17:26:18 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3480 !!! WARNING: ASN 385 has a net charge of 0.5000 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: 0.5599685 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): 36.07000 95.07800 ymin,ymax (A): 17.00100 80.57600 zmin,zma (A): -21.95600 25.40100 x,y,z range (A): 59.00800 63.57500 47.35700 scale (grids/A): 0.5599685 object centre (A): 65.57401 48.78850 1.722499 number of atom coordinates read : 3480 total number of charged atoms : 3333 net assigned charge : -6.999964 assigned positive charge : 525.0460 centred at (gu) : 90.52479 89.89128 89.52496 assigned negative charge : -532.0479 centred at (gu) : 90.57656 89.85491 89.45786 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7210 nv = 96 ne = 84 npr = 69567 no. pairs analyzed = 69567 no. exposed pairs = 4510 no. arc points = 30355 no. surface atoms = 1509 nbur = 1971 mkacc time = 0.1600000 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 = 1.540000 m= 318 mr = 3865 m= 0 mr = 10 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3068 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9234 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8283912E-09 1.2773307E-10 midg,1,midg; midg,igrid,midg -1.2499750E-09 -2.4845892E-10 1,midg,midg; igrid,midg,midg -5.0027052E-11 -1.6160734E-09 gauss-seidel spectral radius is 0.9835881 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 17:26:19 rms-change max change #iterations 9.3507558E-02 13.40738 at 10iterations 6.7464854E-03 0.9932132 at 20iterations 5.0443009E-04 0.1037002 at 30iterations 5.7670226E-05 8.7716579E-03 at 40iterations 1.3430586E-05 2.0442009E-03 at 50iterations finished qdiffx linear iterations at : 17:26:23 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 1.3430586E-05 2.0442009E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.260000 DelPhi exited at 17:26:23 4.262u 0.251s 0:04.87 92.6% 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 Sat Oct 8 2011 at 17:26:23 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3480 !!! WARNING: ASN 385 has a net charge of 0.5000 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: 1.679906 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): 36.07000 95.07800 ymin,ymax (A): 17.00100 80.57600 zmin,zma (A): -21.95600 25.40100 x,y,z range (A): 59.00800 63.57500 47.35700 scale (grids/A): 1.679906 object centre (A): 65.57401 48.78850 1.722499 number of atom coordinates read : 3480 total number of charged atoms : 3333 net assigned charge : -6.999964 assigned positive charge : 525.0460 centred at (gu) : 91.57386 89.67286 88.57397 assigned negative charge : -532.0479 centred at (gu) : 91.72926 89.56423 88.37298 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30355 grid for indexing accessible points = 1.400000 m= 27308 mr = 54753 m= 3255 mr = 19277 m= 104 mr = 1713 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 509 time to turn everything in is 0.5900000 number of dielectric boundary points 33920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 25627 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) : 0.5599685 object centre at (A) : 65.57401 48.78850 1.722499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3176429E-02 -5.9296825E-04 midg,1,midg; midg,igrid,midg 3.4828451E-03 2.0727072E-02 1,midg,midg; igrid,midg,midg -1.3830662E-02 -1.5795780E-02 gauss-seidel spectral radius is 0.9983387 estimated iterations to convergence 195 setup time was (sec) 0.9300000 now iterating at: 17:26:25 rms-change max change #iterations 3.913420 165.2814 at 10iterations 1.689767 55.25076 at 20iterations 0.7316238 28.55323 at 30iterations 0.3167065 10.81387 at 40iterations 0.1374015 4.389603 at 50iterations 5.9419766E-02 2.124251 at 60iterations 2.5831545E-02 0.8011856 at 70iterations 1.1228220E-02 0.3608656 at 80iterations 4.8683286E-03 0.1603813 at 90iterations 2.1181700E-03 6.9057465E-02 at 100iterations 9.2576334E-04 2.7153015E-02 at 110iterations 4.0747385E-04 1.2876511E-02 at 120iterations finished qdiffx linear iterations at : 17:26:33 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 4.0747385E-04 1.2876511E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 17:26:34 9.822u 0.253s 0:10.36 97.2% 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 Sat Oct 8 2011 at 17:26:34 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3480 !!! WARNING: ASN 385 has a net charge of 0.5000 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: 2.519858 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): 36.07000 95.07800 ymin,ymax (A): 17.00100 80.57600 zmin,zma (A): -21.95600 25.40100 x,y,z range (A): 59.00800 63.57500 47.35700 scale (grids/A): 2.519858 object centre (A): 65.57401 48.78850 1.722499 number of atom coordinates read : 3480 total number of charged atoms : 3333 net assigned charge : -6.999964 assigned positive charge : 525.0460 centred at (gu) : 92.36044 89.50916 87.86050 assigned negative charge : -532.0479 centred at (gu) : 92.59388 89.34618 87.55927 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 183140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30355 grid for indexing accessible points = 1.400000 m= 91431 mr = 133327 m= 28543 mr = 73409 m= 5147 mr = 21950 m= 451 mr = 3458 m= 15 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1726 time to turn everything in is 1.490000 number of dielectric boundary points 76406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 26644 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) : 1.679906 object centre at (A) : 65.57401 48.78850 1.722499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1731638 2.7681040E-02 midg,1,midg; midg,igrid,midg 0.3922538 0.6286885 1,midg,midg; igrid,midg,midg -0.1482066 -0.1428994 gauss-seidel spectral radius is 0.9991942 estimated iterations to convergence 278 setup time was (sec) 1.830000 now iterating at: 17:26:36 rms-change max change #iterations 9.940725 284.4190 at 10iterations 5.698223 132.8531 at 20iterations 3.254743 73.08041 at 30iterations 1.848029 38.67677 at 40iterations 1.049072 22.39951 at 50iterations 0.5917141 11.38461 at 60iterations 0.3344589 6.294861 at 70iterations 0.1881079 3.799111 at 80iterations 0.1060674 2.063079 at 90iterations 5.9566185E-02 1.148685 at 100iterations 3.3489157E-02 0.6389542 at 110iterations 1.8833514E-02 0.3841438 at 120iterations 1.0597914E-02 0.2025394 at 130iterations 5.9495852E-03 0.1030750 at 140iterations 3.3515459E-03 6.4725876E-02 at 150iterations 1.8876370E-03 3.4363270E-02 at 160iterations 1.0730404E-03 2.0881653E-02 at 170iterations 6.1288930E-04 1.0976791E-02 at 180iterations finished qdiffx linear iterations at : 17:26:50 total time elapsed so far: 15.59000 # loops : 180 mean,max change (kT/e) : 6.1288930E-04 1.0976791E-02 energy calculations done at 15.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.77000 DelPhi exited at 17:26:50 15.773u 0.271s 0:16.31 98.3% 0+0k 0+0io 0pf+0w