Wed Dec 28 11:02:13 PST 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 Wed Dec 28 2011 at 11:02:13 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 0.5557637 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): -35.28800 12.48300 ymin,ymax (A): -1.056000 41.86700 zmin,zma (A): -2.576000 61.48000 x,y,z range (A): 47.77100 42.92300 64.05600 scale (grids/A): 0.5557637 object centre (A): -11.40250 20.40550 29.45200 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 287.3841 centred at (gu) : 89.72083 90.10825 89.22914 assigned negative charge : -283.3844 centred at (gu) : 89.62547 90.28659 89.19789 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4157 nv = 96 ne = 84 npr = 38349 no. pairs analyzed = 38349 no. exposed pairs = 2526 no. arc points = 18085 no. surface atoms = 858 nbur = 1090 mkacc time = 0.1100000 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 = 1.568000 m= 155 mr = 2134 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1855 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 5138 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1249330E-10 4.6401927E-10 midg,1,midg; midg,igrid,midg 1.3903414E-09 -7.5798579E-10 1,midg,midg; igrid,midg,midg -2.3325838E-10 8.7915952E-10 gauss-seidel spectral radius is 0.9832256 estimated iterations to convergence 64 setup time was (sec) 0.8000000 now iterating at: 11:02:14 rms-change max change #iterations 6.4404272E-02 12.69502 at 10iterations 4.4376599E-03 0.9902306 at 20iterations 3.0809361E-04 6.7340851E-02 at 30iterations 2.1567943E-05 4.3008327E-03 at 40iterations 1.5028079E-06 3.0517578E-04 at 50iterations finished qdiffx linear iterations at : 11:02:22 total time elapsed so far: 8.730000 # loops : 50 mean,max change (kT/e) : 1.5028079E-06 3.0517578E-04 energy calculations done at 8.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 11:02:23 8.894u 0.694s 0:10.11 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 Wed Dec 28 2011 at 11:02:23 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 1.667291 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): -35.28800 12.48300 ymin,ymax (A): -1.056000 41.86700 zmin,zma (A): -2.576000 61.48000 x,y,z range (A): 47.77100 42.92300 64.05600 scale (grids/A): 1.667291 object centre (A): -11.40250 20.40550 29.45200 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 287.3841 centred at (gu) : 89.16247 90.32499 87.68735 assigned negative charge : -283.3844 centred at (gu) : 88.87664 90.86008 87.59384 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 45037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18085 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14984 mr = 30076 m= 1689 mr = 10840 m= 42 mr = 941 m= 0 mr = 1 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 273 time to turn everything in is 0.4200000 number of dielectric boundary points 19894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14008 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) : 0.5557637 object centre at (A) : -11.40250 20.40550 29.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0901451E-02 1.9618640E-02 midg,1,midg; midg,igrid,midg 5.4449113E-03 -7.3198956E-03 1,midg,midg; igrid,midg,midg -1.5188984E-03 1.5737978E-03 gauss-seidel spectral radius is 0.9981467 estimated iterations to convergence 185 setup time was (sec) 0.7400000 now iterating at: 11:02:25 rms-change max change #iterations 2.732791 151.2933 at 10iterations 1.119414 48.22396 at 20iterations 0.4616414 20.57286 at 30iterations 0.1905923 8.741554 at 40iterations 7.8702725E-02 3.447030 at 50iterations 3.2454140E-02 1.457451 at 60iterations 1.3442423E-02 0.5482140 at 70iterations 5.5409377E-03 0.2902527 at 80iterations 2.2884500E-03 0.1000481 at 90iterations 9.4384386E-04 3.8690567E-02 at 100iterations 3.8993376E-04 1.6582489E-02 at 110iterations 1.6081211E-04 6.5231323E-03 at 120iterations finished qdiffx linear iterations at : 11:02:37 total time elapsed so far: 12.37000 # loops : 120 mean,max change (kT/e) : 1.6081211E-04 6.5231323E-03 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 11:02:38 12.541u 0.665s 0:14.89 88.6% 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 Wed Dec 28 2011 at 11:02:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 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: 2.500937 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): -35.28800 12.48300 ymin,ymax (A): -1.056000 41.86700 zmin,zma (A): -2.576000 61.48000 x,y,z range (A): 47.77100 42.92300 64.05600 scale (grids/A): 2.500937 object centre (A): -11.40250 20.40550 29.45200 number of atom coordinates read : 1948 total number of charged atoms : 1818 net assigned charge : 4.000004 assigned positive charge : 287.3841 centred at (gu) : 88.74367 90.48748 86.53099 assigned negative charge : -283.3844 centred at (gu) : 88.31496 91.29018 86.39075 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 104459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18085 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50119 mr = 73472 m= 16026 mr = 40429 m= 2784 mr = 12746 m= 213 mr = 1983 m= 5 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 793 time to turn everything in is 1.110000 number of dielectric boundary points 44879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 14538 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) : 1.667291 object centre at (A) : -11.40250 20.40550 29.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2814267 0.2006908 midg,1,midg; midg,igrid,midg 6.0191657E-02 -0.1168538 1,midg,midg; igrid,midg,midg -4.0956721E-02 2.0863816E-02 gauss-seidel spectral radius is 0.9990947 estimated iterations to convergence 263 setup time was (sec) 1.690000 now iterating at: 11:02:41 rms-change max change #iterations 6.826718 269.7001 at 10iterations 3.709498 102.0118 at 20iterations 2.011982 49.78702 at 30iterations 1.086400 26.39313 at 40iterations 0.5881078 13.62463 at 50iterations 0.3180323 7.699991 at 60iterations 0.1713342 4.121830 at 70iterations 9.2491291E-02 2.305930 at 80iterations 4.9931277E-02 1.253839 at 90iterations 2.6916454E-02 0.6277046 at 100iterations 1.4506987E-02 0.3512011 at 110iterations 7.8539578E-03 0.1918697 at 120iterations 4.2373450E-03 0.1034622 at 130iterations 2.2860414E-03 5.6533813E-02 at 140iterations 1.2334014E-03 2.8549671E-02 at 150iterations 6.6446204E-04 1.8542290E-02 at 160iterations 3.5948344E-04 8.9187622E-03 at 170iterations 1.9403033E-04 5.0759315E-03 at 180iterations finished qdiffx linear iterations at : 11:03:09 total time elapsed so far: 29.71000 # loops : 180 mean,max change (kT/e) : 1.9403033E-04 5.0759315E-03 energy calculations done at 29.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.88000 DelPhi exited at 11:03:09 29.883u 0.861s 0:31.16 98.6% 0+0k 0+0io 0pf+0w