Mon Oct 10 10:51:22 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 Mon Oct 10 2011 at 10:51:22 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 = 5173 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5407787 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): -9.375000 55.39900 ymin,ymax (A): -51.39700 12.30300 zmin,zma (A): -19.05600 46.77500 x,y,z range (A): 64.77400 63.70000 65.83099 scale (grids/A): 0.5407787 object centre (A): 23.01200 -19.54700 13.85950 number of atom coordinates read : 5173 total number of charged atoms : 5017 net assigned charge : 6.000049 assigned positive charge : 816.1545 centred at (gu) : 89.84407 91.56023 88.86828 assigned negative charge : -810.1617 centred at (gu) : 89.83764 91.56239 88.90813 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9911 nv = 96 ne = 84 npr = 101601 no. pairs analyzed = 101601 no. exposed pairs = 6366 no. arc points = 42213 no. surface atoms = 2143 nbur = 3030 mkacc time = 0.1700000 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= 409 mr = 5546 m= 1 mr = 28 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 0.3500000 number of dielectric boundary points 4747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4430 ## 574 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 13096 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1767483E-10 -7.1286269E-11 midg,1,midg; midg,igrid,midg 2.1947755E-10 4.0451312E-10 1,midg,midg; igrid,midg,midg 2.4318308E-10 3.4827152E-10 gauss-seidel spectral radius is 0.9825349 estimated iterations to convergence 62 setup time was (sec) 0.5400000 now iterating at: 10:51:23 rms-change max change #iterations 9.3140721E-02 11.94159 at 10iterations 6.5327366E-03 1.036026 at 20iterations 1.0281365E-03 0.1514158 at 30iterations 5.0112215E-04 7.1098328E-02 at 40iterations 2.6620398E-04 3.7767410E-02 at 50iterations finished qdiffx linear iterations at : 10:51:26 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.6620398E-04 3.7767410E-02 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 10:51:26 3.595u 0.178s 0:04.09 91.9% 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 10:51:26 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 = 5173 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.622336 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): -9.375000 55.39900 ymin,ymax (A): -51.39700 12.30300 zmin,zma (A): -19.05600 46.77500 x,y,z range (A): 64.77400 63.70000 65.83099 scale (grids/A): 1.622336 object centre (A): 23.01200 -19.54700 13.85950 number of atom coordinates read : 5173 total number of charged atoms : 5017 net assigned charge : 6.000049 assigned positive charge : 816.1545 centred at (gu) : 89.53049 94.67901 86.60322 assigned negative charge : -810.1617 centred at (gu) : 89.51310 94.68684 86.72440 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 111821 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42213 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37051 mr = 80319 m= 3787 mr = 26427 m= 114 mr = 1839 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 823 time to turn everything in is 0.5400000 number of dielectric boundary points 44176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 494 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 38234 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) : 0.5407787 object centre at (A) : 23.01200 -19.54700 13.85950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5413529E-03 -4.5461804E-02 midg,1,midg; midg,igrid,midg 3.2736296E-03 6.1705434E-03 1,midg,midg; igrid,midg,midg -4.8700180E-03 2.0059779E-02 gauss-seidel spectral radius is 0.9983675 estimated iterations to convergence 196 setup time was (sec) 0.7600000 now iterating at: 10:51:27 rms-change max change #iterations 4.624240 154.2448 at 10iterations 2.020588 66.28284 at 20iterations 0.8819892 24.82586 at 30iterations 0.3854842 11.34040 at 40iterations 0.1685838 5.005321 at 50iterations 7.3697373E-02 2.098852 at 60iterations 3.2314084E-02 0.8834743 at 70iterations 1.4190254E-02 0.4086627 at 80iterations 6.2750257E-03 0.1767502 at 90iterations 2.8408116E-03 8.0338717E-02 at 100iterations 1.3750419E-03 4.5754135E-02 at 110iterations 7.6216680E-04 2.5749207E-02 at 120iterations finished qdiffx linear iterations at : 10:51:35 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 7.6216680E-04 2.5749207E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 10:51:35 8.190u 0.194s 0:08.73 95.9% 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 10:51:35 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 = 5173 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.433504 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): -9.375000 55.39900 ymin,ymax (A): -51.39700 12.30300 zmin,zma (A): -19.05600 46.77500 x,y,z range (A): 64.77400 63.70000 65.83099 scale (grids/A): 2.433504 object centre (A): 23.01200 -19.54700 13.85950 number of atom coordinates read : 5173 total number of charged atoms : 5017 net assigned charge : 6.000049 assigned positive charge : 816.1545 centred at (gu) : 89.29528 97.01807 84.90440 assigned negative charge : -810.1617 centred at (gu) : 89.26964 97.03023 85.08648 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 260000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42213 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 128204 mr = 195419 m= 36946 mr = 104104 m= 5857 mr = 28164 m= 414 mr = 3814 m= 5 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 2707 time to turn everything in is 1.340000 number of dielectric boundary points 99716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 40098 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) : 1.622336 object centre at (A) : 23.01200 -19.54700 13.85950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9828754E-02 -1.027202 midg,1,midg; midg,igrid,midg 5.1471967E-02 3.1022264E-03 1,midg,midg; igrid,midg,midg -2.3050841E-02 0.3591363 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 1.590000 now iterating at: 10:51:37 rms-change max change #iterations 11.99969 319.4739 at 10iterations 7.048839 172.0317 at 20iterations 4.108866 81.19038 at 30iterations 2.390101 47.57643 at 40iterations 1.379228 24.18394 at 50iterations 0.7952958 15.46991 at 60iterations 0.4572667 8.667189 at 70iterations 0.2628223 4.833922 at 80iterations 0.1508904 2.452827 at 90iterations 8.6334176E-02 1.490005 at 100iterations 4.9413633E-02 0.8267899 at 110iterations 2.8266646E-02 0.4787827 at 120iterations 1.6157821E-02 0.3029060 at 130iterations 9.2532113E-03 0.1650028 at 140iterations 5.2808844E-03 8.6290359E-02 at 150iterations 3.0280196E-03 5.1764011E-02 at 160iterations 1.7424300E-03 2.8555870E-02 at 170iterations 1.0109477E-03 1.6250610E-02 at 180iterations finished qdiffx linear iterations at : 10:51:49 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 1.0109477E-03 1.6250610E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.59000 DelPhi exited at 10:51:49 13.596u 0.222s 0:14.16 97.5% 0+0k 0+0io 0pf+0w