Sat Oct 8 12:39:47 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 Sat Oct 8 2011 at 12:39:47 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 = 2327 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: 0.6021345 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): -22.37400 17.86400 ymin,ymax (A): -18.07300 31.80400 zmin,zma (A): -76.72800 -17.60500 x,y,z range (A): 40.23800 49.87700 59.12300 scale (grids/A): 0.6021345 object centre (A): -2.255000 6.865499 -47.16650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 90.05891 89.61359 90.94714 assigned negative charge : -311.9023 centred at (gu) : 90.11342 89.69115 90.71964 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5638 nv = 96 ne = 84 npr = 49570 no. pairs analyzed = 49570 no. exposed pairs = 3141 no. arc points = 22033 no. surface atoms = 1077 nbur = 1250 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 2689 m= 0 mr = 19 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2141 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6939 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2003633E-09 9.6830357E-09 midg,1,midg; midg,igrid,midg 3.5498944E-09 -1.4679428E-09 1,midg,midg; igrid,midg,midg 2.5058691E-09 -8.8795882E-10 gauss-seidel spectral radius is 0.9857107 estimated iterations to convergence 69 setup time was (sec) 0.5600000 now iterating at: 12:39:48 rms-change max change #iterations 9.6721403E-02 16.78566 at 10iterations 8.8947341E-03 1.369011 at 20iterations 1.7548308E-03 0.3258915 at 30iterations 6.7960680E-04 0.1350861 at 40iterations 2.8435569E-04 5.6793213E-02 at 50iterations finished qdiffx linear iterations at : 12:39:52 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 2.8435569E-04 5.6793213E-02 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 12:39:52 4.444u 0.405s 0:05.11 94.7% 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 12:39:52 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 = 2327 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: 1.806403 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): -22.37400 17.86400 ymin,ymax (A): -18.07300 31.80400 zmin,zma (A): -76.72800 -17.60500 x,y,z range (A): 40.23800 49.87700 59.12300 scale (grids/A): 1.806403 object centre (A): -2.255000 6.865499 -47.16650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 90.17662 88.84061 92.84131 assigned negative charge : -311.9023 centred at (gu) : 90.34042 89.07367 92.15923 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61052 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22033 grid for indexing accessible points = 1.400000 m= 19696 mr = 39573 m= 2741 mr = 12619 m= 103 mr = 1457 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 29919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17183 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) : 0.6021345 object centre at (A) : -2.255000 6.865499 -47.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0037601E-02 4.1890927E-02 midg,1,midg; midg,igrid,midg 3.7121386E-03 6.6759254E-05 1,midg,midg; igrid,midg,midg 3.9176745E-03 1.1239309E-03 gauss-seidel spectral radius is 0.9984675 estimated iterations to convergence 203 setup time was (sec) 0.8400000 now iterating at: 12:39:53 rms-change max change #iterations 3.380061 159.9005 at 10iterations 1.503457 55.27728 at 20iterations 0.6705151 25.60104 at 30iterations 0.3015357 11.70716 at 40iterations 0.1349211 4.975315 at 50iterations 6.0318578E-02 2.068672 at 60iterations 2.7404975E-02 0.9770205 at 70iterations 1.2696027E-02 0.4886665 at 80iterations 6.1623752E-03 0.2354765 at 90iterations 3.2544679E-03 0.1386223 at 100iterations 1.9508881E-03 8.6181641E-02 at 110iterations 1.3128942E-03 5.4706573E-02 at 120iterations finished qdiffx linear iterations at : 12:40:03 total time elapsed so far: 10.31000 # loops : 120 mean,max change (kT/e) : 1.3128942E-03 5.4706573E-02 energy calculations done at 10.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 12:40:03 10.479u 0.476s 0:11.22 97.5% 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 Sat Oct 8 2011 at 12:40:03 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 = 2327 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: 2.709605 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): -22.37400 17.86400 ymin,ymax (A): -18.07300 31.80400 zmin,zma (A): -76.72800 -17.60500 x,y,z range (A): 40.23800 49.87700 59.12300 scale (grids/A): 2.709605 object centre (A): -2.255000 6.865499 -47.16650 number of atom coordinates read : 2327 total number of charged atoms : 2193 net assigned charge : 2.000007 assigned positive charge : 313.9017 centred at (gu) : 90.26493 88.26078 94.26200 assigned negative charge : -311.9023 centred at (gu) : 90.51067 88.61056 93.23885 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 141312 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22033 grid for indexing accessible points = 1.400000 m= 64248 mr = 97070 m= 21425 mr = 48857 m= 4618 mr = 15397 m= 494 mr = 3089 m= 20 mr = 292 m= 0 mr = 6 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 67406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 17542 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) : 1.806403 object centre at (A) : -2.255000 6.865499 -47.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2017200 0.5920996 midg,1,midg; midg,igrid,midg 2.4890482E-02 -8.0186697E-03 1,midg,midg; igrid,midg,midg 1.9867200E-02 4.5776350E-04 gauss-seidel spectral radius is 0.9992130 estimated iterations to convergence 281 setup time was (sec) 1.620000 now iterating at: 12:40:05 rms-change max change #iterations 8.215281 312.2452 at 10iterations 4.797334 144.9197 at 20iterations 2.757969 64.85987 at 30iterations 1.584354 34.59917 at 40iterations 0.9058023 20.47076 at 50iterations 0.5170013 13.30353 at 60iterations 0.2948449 5.934517 at 70iterations 0.1672685 3.797788 at 80iterations 9.5015600E-02 1.962410 at 90iterations 5.3996716E-02 1.117455 at 100iterations 3.0603001E-02 0.7132797 at 110iterations 1.7410660E-02 0.3519374 at 120iterations 9.9419756E-03 0.2129555 at 130iterations 5.7317046E-03 0.1239719 at 140iterations 3.3558640E-03 8.0924988E-02 at 150iterations 2.0335477E-03 5.1532745E-02 at 160iterations 1.3069161E-03 3.3630371E-02 at 170iterations 9.0666563E-04 2.2674561E-02 at 180iterations finished qdiffx linear iterations at : 12:40:21 total time elapsed so far: 17.20000 # loops : 180 mean,max change (kT/e) : 9.0666563E-04 2.2674561E-02 energy calculations done at 17.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.36000 DelPhi exited at 12:40:22 17.369u 0.495s 0:18.15 98.3% 0+0k 0+0io 0pf+0w