Mon Oct 10 18:36:29 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 18:36:29 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2236 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: 0.6896685 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): 28.39100 73.73900 ymin,ymax (A): 16.05100 65.73600 zmin,zma (A): 4.919000 56.53800 x,y,z range (A): 45.34800 49.68500 51.61900 scale (grids/A): 0.6896685 object centre (A): 51.06500 40.89350 30.72850 number of atom coordinates read : 2236 total number of charged atoms : 2100 net assigned charge : 2.500006 assigned positive charge : 333.0102 centred at (gu) : 89.46535 88.27380 88.72375 assigned negative charge : -330.5107 centred at (gu) : 89.43695 88.43258 88.63808 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7006 nv = 96 ne = 84 npr = 46041 no. pairs analyzed = 46041 no. exposed pairs = 2784 no. arc points = 19508 no. surface atoms = 940 nbur = 1296 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 3779 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 130 time to turn everything in is 0.1800000 number of dielectric boundary points 3593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1740 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2225860E-08 3.3056839E-08 midg,1,midg; midg,igrid,midg 9.5786397E-08 -3.0058182E-08 1,midg,midg; igrid,midg,midg 3.5149998E-09 2.0664267E-08 gauss-seidel spectral radius is 0.9890655 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 18:36:30 rms-change max change #iterations 0.1886213 25.46623 at 10iterations 2.2020759E-02 3.562811 at 20iterations 2.5708240E-03 0.3310614 at 30iterations 3.0384539E-04 4.3057442E-02 at 40iterations 3.5688779E-05 4.8942566E-03 at 50iterations finished qdiffx linear iterations at : 18:36:33 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 3.5688779E-05 4.8942566E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 18:36:33 3.408u 0.163s 0:03.92 90.8% 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 18:36:33 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2236 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: 2.069005 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): 28.39100 73.73900 ymin,ymax (A): 16.05100 65.73600 zmin,zma (A): 4.919000 56.53800 x,y,z range (A): 45.34800 49.68500 51.61900 scale (grids/A): 2.069005 object centre (A): 51.06500 40.89350 30.72850 number of atom coordinates read : 2236 total number of charged atoms : 2100 net assigned charge : 2.500006 assigned positive charge : 333.0102 centred at (gu) : 88.39555 84.82072 86.17084 assigned negative charge : -330.5107 centred at (gu) : 88.31087 85.29739 85.91405 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74665 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19508 grid for indexing accessible points = 1.400000 m= 27828 mr = 50966 m= 5329 mr = 20616 m= 426 mr = 3482 m= 13 mr = 213 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 3456 time to turn everything in is 0.4000000 number of dielectric boundary points 32982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16673 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) : 0.6896685 object centre at (A) : 51.06500 40.89350 30.72850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1070055E-02 4.8474431E-02 midg,1,midg; midg,igrid,midg 4.7203429E-02 -2.1454969E-02 1,midg,midg; igrid,midg,midg 1.5268638E-02 1.5007916E-02 gauss-seidel spectral radius is 0.9987966 estimated iterations to convergence 228 setup time was (sec) 0.6200000 now iterating at: 18:36:34 rms-change max change #iterations 4.567880 220.7163 at 10iterations 2.230243 76.63689 at 20iterations 1.091464 36.34990 at 30iterations 0.5363666 15.91721 at 40iterations 0.2631482 8.165764 at 50iterations 0.1289420 3.885262 at 60iterations 6.3283086E-02 1.856644 at 70iterations 3.0903561E-02 1.040024 at 80iterations 1.5173052E-02 0.4403839 at 90iterations 7.4480753E-03 0.2201681 at 100iterations 3.6442264E-03 0.1155796 at 110iterations 1.7938185E-03 5.6462765E-02 at 120iterations finished qdiffx linear iterations at : 18:36:41 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.7938185E-03 5.6462765E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 18:36:42 7.913u 0.193s 0:08.56 94.6% 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 Mon Oct 10 2011 at 18:36:42 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2236 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: 3.103508 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): 28.39100 73.73900 ymin,ymax (A): 16.05100 65.73600 zmin,zma (A): 4.919000 56.53800 x,y,z range (A): 45.34800 49.68500 51.61900 scale (grids/A): 3.103508 object centre (A): 51.06500 40.89350 30.72850 number of atom coordinates read : 2236 total number of charged atoms : 2100 net assigned charge : 2.500006 assigned positive charge : 333.0102 centred at (gu) : 87.59318 82.23088 84.25614 assigned negative charge : -330.5107 centred at (gu) : 87.46620 82.94601 83.87089 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 172482 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19508 grid for indexing accessible points = 1.400000 m= 87330 mr = 123776 m= 35095 mr = 71016 m= 9815 mr = 28577 m= 1722 mr = 7632 m= 167 mr = 1243 m= 12 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 11817 time to turn everything in is 1.150000 number of dielectric boundary points 74288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 16796 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) : 2.069005 object centre at (A) : 51.06500 40.89350 30.72850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7613540E-04 0.9132137 midg,1,midg; midg,igrid,midg 0.4176538 -0.1235913 1,midg,midg; igrid,midg,midg 0.2044210 4.3278951E-02 gauss-seidel spectral radius is 0.9992940 estimated iterations to convergence 297 setup time was (sec) 1.390000 now iterating at: 18:36:44 rms-change max change #iterations 10.39305 379.2610 at 10iterations 6.134832 133.3874 at 20iterations 3.615093 78.80194 at 30iterations 2.117046 56.04281 at 40iterations 1.238349 22.55323 at 50iterations 0.7261209 14.01717 at 60iterations 0.4234634 7.886204 at 70iterations 0.2470830 4.256413 at 80iterations 0.1438967 2.537079 at 90iterations 8.4071033E-02 1.509332 at 100iterations 4.8921250E-02 0.8155413 at 110iterations 2.8497264E-02 0.5499229 at 120iterations 1.6620962E-02 0.2770691 at 130iterations 9.6783582E-03 0.1680412 at 140iterations 5.6369430E-03 9.0526581E-02 at 150iterations 3.2891093E-03 5.6434631E-02 at 160iterations 1.9160908E-03 3.2416105E-02 at 170iterations 1.1208947E-03 1.9641876E-02 at 180iterations finished qdiffx linear iterations at : 18:36:55 total time elapsed so far: 12.85000 # loops : 180 mean,max change (kT/e) : 1.1208947E-03 1.9641876E-02 energy calculations done at 12.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 18:36:55 12.988u 0.211s 0:13.53 97.4% 0+0k 0+0io 0pf+0w