Mon Oct 10 09:45:05 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 Mon Oct 10 2011 at 09:45:05 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2699 !!! WARNING: HIT 224 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5918930 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): -20.31500 34.89000 ymin,ymax (A): -61.15500 -1.009000 zmin,zma (A): -1.765000 54.26900 x,y,z range (A): 55.20500 60.14600 56.03400 scale (grids/A): 0.5918930 object centre (A): 7.287499 -31.08200 26.25200 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 6.014013 assigned positive charge : 392.3833 centred at (gu) : 89.00867 88.19509 89.43935 assigned negative charge : -386.3695 centred at (gu) : 89.06410 88.02775 89.39817 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6565 nv = 96 ne = 84 npr = 51445 no. pairs analyzed = 51445 no. exposed pairs = 4347 no. arc points = 31298 no. surface atoms = 1425 nbur = 1274 mkacc time = 9.0000004E-02 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 = 1.456000 m= 380 mr = 2798 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3004 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0043382E-09 2.8182920E-09 midg,1,midg; midg,igrid,midg -4.2478758E-09 4.4047090E-09 1,midg,midg; igrid,midg,midg 4.5099324E-09 4.0704667E-10 gauss-seidel spectral radius is 0.9852638 estimated iterations to convergence 68 setup time was (sec) 0.4100000 now iterating at: 09:45:06 rms-change max change #iterations 0.1004843 16.10890 at 10iterations 8.3843805E-03 1.380653 at 20iterations 7.1381684E-04 0.1160755 at 30iterations 7.3713636E-05 1.5092850E-02 at 40iterations 1.1871890E-05 2.7885437E-03 at 50iterations finished qdiffx linear iterations at : 09:45:09 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.1871890E-05 2.7885437E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 09:45:09 3.503u 0.310s 0:04.16 91.5% 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 Mon Oct 10 2011 at 09:45:09 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2699 !!! WARNING: HIT 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.775679 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): -20.31500 34.89000 ymin,ymax (A): -61.15500 -1.009000 zmin,zma (A): -1.765000 54.26900 x,y,z range (A): 55.20500 60.14600 56.03400 scale (grids/A): 1.775679 object centre (A): 7.287499 -31.08200 26.25200 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 6.014013 assigned positive charge : 392.3833 centred at (gu) : 87.02552 84.58473 88.31770 assigned negative charge : -386.3695 centred at (gu) : 87.19209 84.08318 88.19425 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 69336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31298 grid for indexing accessible points = 1.400000 m= 23308 mr = 41497 m= 3426 mr = 14675 m= 161 mr = 1589 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 233 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19893 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) : 0.5918930 object centre at (A) : 7.287499 -31.08200 26.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1823602E-03 -8.9559983E-03 midg,1,midg; midg,igrid,midg 2.4330404E-02 3.9392430E-02 1,midg,midg; igrid,midg,midg 2.1144692E-02 1.2028806E-02 gauss-seidel spectral radius is 0.9984767 estimated iterations to convergence 203 setup time was (sec) 0.5900000 now iterating at: 09:45:10 rms-change max change #iterations 3.715391 153.4386 at 10iterations 1.654749 65.79196 at 20iterations 0.7369984 27.84349 at 30iterations 0.3302616 14.04529 at 40iterations 0.1476689 5.517242 at 50iterations 6.5983370E-02 2.362806 at 60iterations 2.9544689E-02 1.086658 at 70iterations 1.3224925E-02 0.4826813 at 80iterations 5.9180399E-03 0.2134724 at 90iterations 2.6499408E-03 9.9441051E-02 at 100iterations 1.1887222E-03 4.5497894E-02 at 110iterations 5.3312286E-04 1.9130230E-02 at 120iterations finished qdiffx linear iterations at : 09:45:17 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 5.3312286E-04 1.9130230E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 09:45:18 7.877u 0.197s 0:08.54 94.3% 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 09:45:18 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2699 !!! WARNING: HIT 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.663519 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): -20.31500 34.89000 ymin,ymax (A): -61.15500 -1.009000 zmin,zma (A): -1.765000 54.26900 x,y,z range (A): 55.20500 60.14600 56.03400 scale (grids/A): 2.663519 object centre (A): 7.287499 -31.08200 26.25200 number of atom coordinates read : 2699 total number of charged atoms : 2552 net assigned charge : 6.014013 assigned positive charge : 392.3833 centred at (gu) : 85.53807 81.87700 87.47644 assigned negative charge : -386.3695 centred at (gu) : 85.78816 81.12470 87.29139 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 159968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31298 grid for indexing accessible points = 1.400000 m= 73974 mr = 102691 m= 26254 mr = 54469 m= 5623 mr = 18751 m= 521 mr = 3451 m= 16 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 86812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 20407 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) : 1.775679 object centre at (A) : 7.287499 -31.08200 26.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3703767E-02 -0.1196912 midg,1,midg; midg,igrid,midg 0.3063907 0.5165210 1,midg,midg; igrid,midg,midg 0.1578320 0.1669041 gauss-seidel spectral radius is 0.9992486 estimated iterations to convergence 288 setup time was (sec) 1.160000 now iterating at: 09:45:19 rms-change max change #iterations 9.474891 309.7194 at 10iterations 5.693655 159.6168 at 20iterations 3.348215 109.8901 at 30iterations 1.963545 56.61039 at 40iterations 1.143167 38.48989 at 50iterations 0.6626534 18.61601 at 60iterations 0.3826655 9.795914 at 70iterations 0.2211006 5.633682 at 80iterations 0.1273906 3.429052 at 90iterations 7.3225945E-02 1.778587 at 100iterations 4.2026699E-02 0.9369926 at 110iterations 2.4103848E-02 0.5474138 at 120iterations 1.3830074E-02 0.2934532 at 130iterations 7.9121841E-03 0.1703625 at 140iterations 4.5386041E-03 0.1019206 at 150iterations 2.6001995E-03 6.0220718E-02 at 160iterations 1.4909006E-03 3.0492783E-02 at 170iterations 8.5395988E-04 1.7503023E-02 at 180iterations finished qdiffx linear iterations at : 09:45:31 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 8.5395988E-04 1.7503023E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 09:45:31 12.857u 0.203s 0:13.41 97.3% 0+0k 0+0io 0pf+0w