Tue Nov 22 14:11:31 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+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 Tue Nov 22 2011 at 14:11:41 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 0.6325403 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 0.6325403 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 285.2440 centred at (gu) : 90.60930 90.00972 90.51276 assigned negative charge : -282.2443 centred at (gu) : 90.51987 90.16592 90.50806 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5260 nv = 96 ne = 84 npr = 39877 no. pairs analyzed = 39877 no. exposed pairs = 2447 no. arc points = 17104 no. surface atoms = 831 nbur = 1111 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 2895 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8421536E-09 4.2436068E-09 midg,1,midg; midg,igrid,midg 1.4060428E-08 -7.5083548E-09 1,midg,midg; igrid,midg,midg -2.3852247E-09 1.0958880E-08 gauss-seidel spectral radius is 0.9869956 estimated iterations to convergence 72 setup time was (sec) 0.4600000 now iterating at: 14:11:46 rms-change max change #iterations 0.1146381 18.90366 at 10iterations 1.1034537E-02 1.817814 at 20iterations 1.0459257E-03 0.1894188 at 30iterations 9.8985875E-05 1.6731262E-02 at 40iterations 9.4614261E-06 1.4762878E-03 at 50iterations finished qdiffx linear iterations at : 14:11:54 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 9.4614261E-06 1.4762878E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:12:01 3.425u 0.196s 0:21.50 16.7% 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 Tue Nov 22 2011 at 14:12:04 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 1.897621 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 1.897621 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 285.2440 centred at (gu) : 91.82807 90.02931 91.53822 assigned negative charge : -282.2443 centred at (gu) : 91.55989 90.49789 91.52432 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 56508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17104 grid for indexing accessible points = 1.400000 m= 21108 mr = 38804 m= 3386 mr = 15964 m= 187 mr = 2160 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 24205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14214 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) : 0.6325403 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3558680E-02 3.3999655E-02 midg,1,midg; midg,igrid,midg 5.4165772E-03 -1.0454757E-02 1,midg,midg; igrid,midg,midg -4.1665016E-03 -1.1926399E-03 gauss-seidel spectral radius is 0.9985476 estimated iterations to convergence 208 setup time was (sec) 0.6900000 now iterating at: 14:12:08 rms-change max change #iterations 3.510682 167.1700 at 10iterations 1.609394 65.73900 at 20iterations 0.7356727 26.03039 at 30iterations 0.3369372 11.34597 at 40iterations 0.1537164 5.309144 at 50iterations 7.0370287E-02 2.598328 at 60iterations 3.2040026E-02 1.116680 at 70iterations 1.4685150E-02 0.5553772 at 80iterations 6.6887960E-03 0.2381573 at 90iterations 3.0657712E-03 0.1115932 at 100iterations 1.3986607E-03 5.1888287E-02 at 110iterations 6.4153865E-04 2.3034096E-02 at 120iterations finished qdiffx linear iterations at : 14:12:28 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 6.4153865E-04 2.3034096E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.270000 DelPhi exited at 14:12:33 7.269u 0.199s 0:30.16 24.7% 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 Tue Nov 22 2011 at 14:12:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1942 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: 2.846431 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 2.846431 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1942 total number of charged atoms : 1810 net assigned charge : 3.000004 assigned positive charge : 285.2440 centred at (gu) : 92.74203 90.04398 92.30740 assigned negative charge : -282.2443 centred at (gu) : 92.33990 90.74690 92.28655 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 130720 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17104 grid for indexing accessible points = 1.400000 m= 67757 mr = 94022 m= 25299 mr = 56053 m= 6103 mr = 20816 m= 865 mr = 4633 m= 57 mr = 603 m= 4 mr = 28 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 54648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 14471 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) : 1.897621 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0734982E-02 0.1915075 midg,1,midg; midg,igrid,midg -2.7478239E-03 -0.1411667 1,midg,midg; igrid,midg,midg -7.2740830E-02 -6.5975115E-02 gauss-seidel spectral radius is 0.9992184 estimated iterations to convergence 282 setup time was (sec) 1.280000 now iterating at: 14:12:48 rms-change max change #iterations 8.236385 393.1075 at 10iterations 4.692672 98.19966 at 20iterations 2.658947 63.87181 at 30iterations 1.506317 43.91593 at 40iterations 0.8507776 20.84274 at 50iterations 0.4806653 9.892845 at 60iterations 0.2714926 5.693254 at 70iterations 0.1532755 3.288343 at 80iterations 8.6681314E-02 1.761871 at 90iterations 4.8936870E-02 1.021355 at 100iterations 2.7730567E-02 0.5467925 at 110iterations 1.5606291E-02 0.3360052 at 120iterations 8.8347010E-03 0.1845548 at 130iterations 4.9756397E-03 0.1026449 at 140iterations 2.8149716E-03 5.6017876E-02 at 150iterations 1.5850952E-03 3.2695532E-02 at 160iterations 8.9544419E-04 1.8669128E-02 at 170iterations 5.0545268E-04 1.1405945E-02 at 180iterations finished qdiffx linear iterations at : 14:13:16 total time elapsed so far: 10.67000 # loops : 180 mean,max change (kT/e) : 5.0545268E-04 1.1405945E-02 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:13:19 10.855u 0.168s 0:40.71 27.0% 0+0k 0+0io 0pf+0w