Wed Feb 15 08:54:44 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:44 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 = 2135 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6591493 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 0.6591493 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2007 net assigned charge : 6.500008 assigned positive charge : 326.6808 centred at (gu) : 88.95655 90.56250 90.24517 assigned negative charge : -320.1811 centred at (gu) : 88.96046 90.64340 90.14817 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6034 nv = 96 ne = 84 npr = 44219 no. pairs analyzed = 44219 no. exposed pairs = 2557 no. arc points = 17558 no. surface atoms = 884 nbur = 1251 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3335 m= 3 mr = 43 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 0.2500000 number of dielectric boundary points 2972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1814 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7258 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5642652E-10 3.3128245E-08 midg,1,midg; midg,igrid,midg 2.5810481E-08 3.4358114E-09 1,midg,midg; igrid,midg,midg 2.0750113E-08 1.2632953E-08 gauss-seidel spectral radius is 0.9880197 estimated iterations to convergence 75 setup time was (sec) 0.4600000 now iterating at: 08:54:45 rms-change max change #iterations 0.1475197 28.12840 at 10iterations 1.5876150E-02 2.040569 at 20iterations 1.7607812E-03 0.2371368 at 30iterations 2.5495503E-04 3.8848877E-02 at 40iterations 5.4327105E-05 8.0242157E-03 at 50iterations finished qdiffx linear iterations at : 08:54:47 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 5.4327105E-05 8.0242157E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.040000 DelPhi exited at 08:54:47 3.045u 0.151s 0:03.54 90.1% 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 Feb 15 2012 at 08:54:48 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 = 2135 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.977448 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 1.977448 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2007 net assigned charge : 6.500008 assigned positive charge : 326.6808 centred at (gu) : 86.86963 91.68747 90.73570 assigned negative charge : -320.1811 centred at (gu) : 86.88148 91.93024 90.44443 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 23525 mr = 45066 m= 3616 mr = 17328 m= 216 mr = 2199 m= 4 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 27179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 15804 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) : 0.6591493 object centre at (A) : 22.28550 9.474001 23.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0600639E-02 2.3683771E-02 midg,1,midg; midg,igrid,midg 2.2947770E-02 5.6265229E-03 1,midg,midg; igrid,midg,midg 7.0259519E-02 1.1684710E-02 gauss-seidel spectral radius is 0.9986728 estimated iterations to convergence 217 setup time was (sec) 0.7500000 now iterating at: 08:54:49 rms-change max change #iterations 4.118381 225.1665 at 10iterations 1.949218 73.32105 at 20iterations 0.9246106 33.68132 at 30iterations 0.4378847 15.12789 at 40iterations 0.2063758 7.142984 at 50iterations 9.8056056E-02 3.224385 at 60iterations 4.6439711E-02 1.760836 at 70iterations 2.1981657E-02 0.6936036 at 80iterations 1.0453956E-02 0.3549271 at 90iterations 4.9871961E-03 0.1764631 at 100iterations 2.3861642E-03 7.7337265E-02 at 110iterations 1.1538947E-03 3.6808014E-02 at 120iterations finished qdiffx linear iterations at : 08:54:55 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 1.1538947E-03 3.6808014E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 08:54:57 6.988u 0.212s 0:09.54 75.3% 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 Feb 15 2012 at 08:54:57 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 = 2135 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: 2.966172 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): -4.719000 49.29000 ymin,ymax (A): -10.86300 29.81100 zmin,zma (A): 0.4179999 47.44400 x,y,z range (A): 54.00900 40.67400 47.02600 scale (grids/A): 2.966172 object centre (A): 22.28550 9.474001 23.93100 number of atom coordinates read : 2135 total number of charged atoms : 2007 net assigned charge : 6.500008 assigned positive charge : 326.6808 centred at (gu) : 85.30428 92.53111 91.10352 assigned negative charge : -320.1811 centred at (gu) : 85.32214 92.89539 90.66659 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 149047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 76020 mr = 109120 m= 27305 mr = 62222 m= 6525 mr = 21898 m= 946 mr = 4780 m= 64 mr = 670 m= 0 mr = 28 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 61189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 16056 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) : 1.977448 object centre at (A) : 22.28550 9.474001 23.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2041440 0.2494615 midg,1,midg; midg,igrid,midg 0.2319697 4.9895797E-02 1,midg,midg; igrid,midg,midg 1.007484 -0.2395293 gauss-seidel spectral radius is 0.9992567 estimated iterations to convergence 289 setup time was (sec) 1.490000 now iterating at: 08:54:59 rms-change max change #iterations 9.440948 381.9446 at 10iterations 5.511891 132.9704 at 20iterations 3.208193 69.91757 at 30iterations 1.867917 37.59213 at 40iterations 1.086619 22.86254 at 50iterations 0.6271802 12.46623 at 60iterations 0.3641735 8.327811 at 70iterations 0.2101648 4.208405 at 80iterations 0.1211952 2.273794 at 90iterations 6.9884330E-02 1.375029 at 100iterations 4.0410645E-02 0.8089638 at 110iterations 2.3352087E-02 0.4439011 at 120iterations 1.3565227E-02 0.2654667 at 130iterations 7.9038637E-03 0.1672039 at 140iterations 4.6658893E-03 8.7759018E-02 at 150iterations 2.8128584E-03 5.8944702E-02 at 160iterations 1.7511860E-03 3.5577774E-02 at 170iterations 1.1410501E-03 2.1190643E-02 at 180iterations finished qdiffx linear iterations at : 08:55:09 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 1.1410501E-03 2.1190643E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 08:55:10 11.997u 0.169s 0:12.58 96.5% 0+0k 0+0io 0pf+0w