Sat Oct 8 11:39:19 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 11:39:19 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4281 !!! WARNING: HIQ 441 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5280410 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): -3.598000 63.82100 ymin,ymax (A): -12.52700 38.30200 zmin,zma (A): -19.50900 45.05500 x,y,z range (A): 67.41901 50.82900 64.56400 scale (grids/A): 0.5280410 object centre (A): 30.11150 12.88750 12.77300 number of atom coordinates read : 4281 total number of charged atoms : 4129 net assigned charge : -4.485949 assigned positive charge : 643.4852 centred at (gu) : 88.63891 89.97974 90.67900 assigned negative charge : -647.9736 centred at (gu) : 88.67073 90.08146 90.69667 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7520 nv = 96 ne = 84 npr = 89943 no. pairs analyzed = 89943 no. exposed pairs = 4877 no. arc points = 32615 no. surface atoms = 1664 nbur = 2617 mkacc time = 0.2100000 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 = 1.596000 m= 287 mr = 4239 m= 0 mr = 15 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 3553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3403 ## 456 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 10124 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3950732E-11 -2.6371372E-10 midg,1,midg; midg,igrid,midg 3.5030226E-10 -6.3104333E-10 1,midg,midg; igrid,midg,midg 2.6820240E-11 -2.0633206E-10 gauss-seidel spectral radius is 0.9816092 estimated iterations to convergence 61 setup time was (sec) 0.6900000 now iterating at: 11:39:20 rms-change max change #iterations 7.4883737E-02 11.33891 at 10iterations 5.2248985E-03 0.9550662 at 20iterations 8.6506666E-04 0.1209450 at 30iterations 2.7833757E-04 3.9928436E-02 at 40iterations 9.5598632E-05 1.4213562E-02 at 50iterations finished qdiffx linear iterations at : 11:39:23 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 9.5598632E-05 1.4213562E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 11:39:24 3.530u 0.165s 0:04.16 88.7% 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 11:39:24 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4281 !!! WARNING: HIQ 441 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.584123 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): -3.598000 63.82100 ymin,ymax (A): -12.52700 38.30200 zmin,zma (A): -19.50900 45.05500 x,y,z range (A): 67.41901 50.82900 64.56400 scale (grids/A): 1.584123 object centre (A): 30.11150 12.88750 12.77300 number of atom coordinates read : 4281 total number of charged atoms : 4129 net assigned charge : -4.485949 assigned positive charge : 643.4852 centred at (gu) : 85.91568 89.93785 92.03611 assigned negative charge : -647.9736 centred at (gu) : 86.01181 90.24397 92.08956 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85513 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32615 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26415 mr = 61701 m= 2549 mr = 18708 m= 42 mr = 1262 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1000 time to turn everything in is 0.6600000 number of dielectric boundary points 32849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 406 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 31402 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) : 0.5280410 object centre at (A) : 30.11150 12.88750 12.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2234923E-03 -1.0614742E-02 midg,1,midg; midg,igrid,midg 3.2151218E-03 -1.4157047E-02 1,midg,midg; igrid,midg,midg 1.2450509E-02 1.0098115E-02 gauss-seidel spectral radius is 0.9981871 estimated iterations to convergence 187 setup time was (sec) 0.9500000 now iterating at: 11:39:25 rms-change max change #iterations 3.857337 169.9085 at 10iterations 1.608385 55.74451 at 20iterations 0.6705917 22.12904 at 30iterations 0.2815697 9.281875 at 40iterations 0.1174356 4.373308 at 50iterations 4.9437512E-02 1.562725 at 60iterations 2.0797577E-02 0.6467609 at 70iterations 8.8649485E-03 0.2719383 at 80iterations 3.8567153E-03 0.1231632 at 90iterations 1.7574156E-03 5.9336424E-02 at 100iterations 8.8130299E-04 3.3384323E-02 at 110iterations 4.9182307E-04 1.6153812E-02 at 120iterations finished qdiffx linear iterations at : 11:39:31 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 4.9182307E-04 1.6153812E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 11:39:32 7.725u 0.196s 0:08.85 89.3% 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 Sat Oct 8 2011 at 11:39:33 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4281 !!! WARNING: HIQ 441 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.376184 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): -3.598000 63.82100 ymin,ymax (A): -12.52700 38.30200 zmin,zma (A): -19.50900 45.05500 x,y,z range (A): 67.41901 50.82900 64.56400 scale (grids/A): 2.376184 object centre (A): 30.11150 12.88750 12.77300 number of atom coordinates read : 4281 total number of charged atoms : 4129 net assigned charge : -4.485949 assigned positive charge : 643.4852 centred at (gu) : 83.87337 89.90649 93.05373 assigned negative charge : -647.9736 centred at (gu) : 84.01761 90.36574 93.13426 start vw surface at 0.2200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 199498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32615 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 93432 mr = 150870 m= 25669 mr = 75681 m= 3945 mr = 19450 m= 202 mr = 2602 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 3220 time to turn everything in is 1.530000 number of dielectric boundary points 74082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 32966 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) : 1.584123 object centre at (A) : 30.11150 12.88750 12.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2378080 -0.2223204 midg,1,midg; midg,igrid,midg 4.6291277E-02 -0.2083247 1,midg,midg; igrid,midg,midg 0.3247495 0.2486419 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 1.830000 now iterating at: 11:39:35 rms-change max change #iterations 10.08492 307.4022 at 10iterations 5.733093 118.8028 at 20iterations 3.245450 66.96180 at 30iterations 1.825919 40.84054 at 40iterations 1.023208 19.02583 at 50iterations 0.5738913 10.90469 at 60iterations 0.3205663 6.987015 at 70iterations 0.1788436 3.458235 at 80iterations 9.9818118E-02 1.843938 at 90iterations 5.5544462E-02 1.112110 at 100iterations 3.0922092E-02 0.6158943 at 110iterations 1.7246904E-02 0.3074646 at 120iterations 9.6219145E-03 0.1852579 at 130iterations 5.3923186E-03 9.6559525E-02 at 140iterations 3.0442395E-03 6.2095642E-02 at 150iterations 1.7340784E-03 3.5526276E-02 at 160iterations 1.0138938E-03 1.8437862E-02 at 170iterations 6.1415322E-04 1.1575699E-02 at 180iterations finished qdiffx linear iterations at : 11:39:45 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 6.1415322E-04 1.1575699E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 11:39:46 12.393u 0.196s 0:13.13 95.8% 0+0k 0+0io 0pf+0w