Mon Oct 10 09:15:17 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 09:15:17 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6536428 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): -4.194000 34.45500 ymin,ymax (A): -3.431000 47.88600 zmin,zma (A): -23.66300 30.80100 x,y,z range (A): 38.64900 51.31700 54.46400 scale (grids/A): 0.6536428 object centre (A): 15.13050 22.22750 3.569000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.27222 92.60315 90.06830 assigned negative charge : -288.0262 centred at (gu) : 90.38177 92.73601 90.00885 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5606 nv = 96 ne = 84 npr = 40849 no. pairs analyzed = 40849 no. exposed pairs = 2463 no. arc points = 17364 no. surface atoms = 831 nbur = 1133 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 326 mr = 3070 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.2700000 number of dielectric boundary points 2824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6663 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7500048E-10 1.4403554E-08 midg,1,midg; midg,igrid,midg 1.3450027E-08 -1.7540778E-08 1,midg,midg; igrid,midg,midg 1.9151338E-08 -7.2206165E-09 gauss-seidel spectral radius is 0.9878126 estimated iterations to convergence 74 setup time was (sec) 0.5000000 now iterating at: 09:15:18 rms-change max change #iterations 0.1382658 21.63121 at 10iterations 1.4422812E-02 2.201336 at 20iterations 1.4928748E-03 0.2227135 at 30iterations 1.5419163E-04 2.4459839E-02 at 40iterations 1.5812226E-05 2.3841858E-03 at 50iterations finished qdiffx linear iterations at : 09:15:20 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.5812226E-05 2.3841858E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 09:15:21 3.308u 0.156s 0:03.76 91.7% 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 Mon Oct 10 2011 at 09:15:21 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.960928 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): -4.194000 34.45500 ymin,ymax (A): -3.431000 47.88600 zmin,zma (A): -23.66300 30.80100 x,y,z range (A): 38.64900 51.31700 54.46400 scale (grids/A): 1.960928 object centre (A): 15.13050 22.22750 3.569000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.81641 97.80940 90.20527 assigned negative charge : -288.0262 centred at (gu) : 91.14548 98.20810 90.02662 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17364 grid for indexing accessible points = 1.400000 m= 21935 mr = 41403 m= 3752 mr = 16594 m= 255 mr = 2501 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1504 time to turn everything in is 0.5000000 number of dielectric boundary points 25859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14469 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) : 0.6536428 object centre at (A) : 15.13050 22.22750 3.569000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2691143E-02 1.5694223E-02 midg,1,midg; midg,igrid,midg 4.6715926E-02 -5.0362260E-03 1,midg,midg; igrid,midg,midg 6.5541277E-03 -7.1084872E-03 gauss-seidel spectral radius is 0.9986311 estimated iterations to convergence 214 setup time was (sec) 0.7800000 now iterating at: 09:15:22 rms-change max change #iterations 3.830018 165.1864 at 10iterations 1.790646 64.68964 at 20iterations 0.8385444 30.37258 at 30iterations 0.3913926 14.14794 at 40iterations 0.1833488 6.379233 at 50iterations 8.5284099E-02 3.026199 at 60iterations 4.0091097E-02 1.364075 at 70iterations 1.8682782E-02 0.6855812 at 80iterations 8.7649999E-03 0.2859062 at 90iterations 4.0888893E-03 0.1367447 at 100iterations 1.9066313E-03 6.7177773E-02 at 110iterations 8.9186139E-04 2.9731274E-02 at 120iterations finished qdiffx linear iterations at : 09:15:28 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 8.9186139E-04 2.9731274E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 09:15:29 7.416u 0.155s 0:07.87 96.0% 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 09:15:29 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.941392 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): -4.194000 34.45500 ymin,ymax (A): -3.431000 47.88600 zmin,zma (A): -23.66300 30.80100 x,y,z range (A): 38.64900 51.31700 54.46400 scale (grids/A): 2.941392 object centre (A): 15.13050 22.22750 3.569000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 91.22468 101.7140 90.30780 assigned negative charge : -288.0262 centred at (gu) : 91.71828 102.3122 90.03995 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 139629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17364 grid for indexing accessible points = 1.400000 m= 70338 mr = 100296 m= 26503 mr = 57917 m= 6995 mr = 21897 m= 1117 mr = 5459 m= 50 mr = 758 m= 2 mr = 10 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 5294 time to turn everything in is 1.190000 number of dielectric boundary points 58298 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 14652 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) : 1.960928 object centre at (A) : 15.13050 22.22750 3.569000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.167520 4.8986737E-02 midg,1,midg; midg,igrid,midg 0.5114504 -0.1191991 1,midg,midg; igrid,midg,midg 2.9510483E-02 -4.3351557E-02 gauss-seidel spectral radius is 0.9992448 estimated iterations to convergence 287 setup time was (sec) 1.470000 now iterating at: 09:15:30 rms-change max change #iterations 8.858714 332.4678 at 10iterations 5.074750 114.3088 at 20iterations 2.897843 61.90321 at 30iterations 1.656047 33.68098 at 40iterations 0.9469740 19.31784 at 50iterations 0.5384549 11.32585 at 60iterations 0.3069840 5.890011 at 70iterations 0.1752293 3.469230 at 80iterations 9.9876225E-02 1.899241 at 90iterations 5.6897152E-02 1.125741 at 100iterations 3.2395337E-02 0.5814800 at 110iterations 1.8470477E-02 0.3392162 at 120iterations 1.0495742E-02 0.2288551 at 130iterations 5.9938561E-03 0.1211243 at 140iterations 3.4127452E-03 6.5343857E-02 at 150iterations 1.9486742E-03 3.8146973E-02 at 160iterations 1.1109009E-03 2.0051956E-02 at 170iterations 6.3347939E-04 1.2279510E-02 at 180iterations finished qdiffx linear iterations at : 09:15:41 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 6.3347939E-04 1.2279510E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 09:15:41 12.051u 0.181s 0:12.56 97.3% 0+0k 0+0io 0pf+0w