Mon Oct 10 11:10:38 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 11:10:38 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 = 2128 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: 0.7427189 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): -21.55600 24.34100 ymin,ymax (A): -7.757000 38.24500 zmin,zma (A): -3.395000 44.53700 x,y,z range (A): 45.89700 46.00200 47.93200 scale (grids/A): 0.7427189 object centre (A): 1.392500 15.24400 20.57100 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 89.15495 89.69743 90.01857 assigned negative charge : -324.1440 centred at (gu) : 89.23419 89.73157 90.22617 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8070 nv = 96 ne = 84 npr = 43749 no. pairs analyzed = 43749 no. exposed pairs = 2726 no. arc points = 19320 no. surface atoms = 921 nbur = 1207 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4447 m= 2 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.2700000 number of dielectric boundary points 4049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1538 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8500 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2678291E-07 -3.2537574E-07 midg,1,midg; midg,igrid,midg -6.0062114E-08 -1.2419116E-07 1,midg,midg; igrid,midg,midg -8.9151211E-09 -1.5472683E-07 gauss-seidel spectral radius is 0.9905576 estimated iterations to convergence 84 setup time was (sec) 0.5600000 now iterating at: 11:10:39 rms-change max change #iterations 0.2465794 37.46339 at 10iterations 3.3303481E-02 4.164482 at 20iterations 4.4575729E-03 0.5775337 at 30iterations 6.1983708E-04 8.1312180E-02 at 40iterations 8.4038817E-05 1.0470390E-02 at 50iterations finished qdiffx linear iterations at : 11:10:43 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 8.4038817E-05 1.0470390E-02 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.630000 DelPhi exited at 11:10:43 4.637u 0.389s 0:05.31 94.3% 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 Mon Oct 10 2011 at 11:10:43 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 = 2128 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: 2.228157 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): -21.55600 24.34100 ymin,ymax (A): -7.757000 38.24500 zmin,zma (A): -3.395000 44.53700 x,y,z range (A): 45.89700 46.00200 47.93200 scale (grids/A): 2.228157 object centre (A): 1.392500 15.24400 20.57100 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 87.46479 89.09236 90.05579 assigned negative charge : -324.1440 centred at (gu) : 87.70255 89.19483 90.67835 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19320 grid for indexing accessible points = 1.400000 m= 33847 mr = 58569 m= 7183 mr = 25697 m= 801 mr = 5011 m= 23 mr = 422 m= 0 mr = 7 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1226 time to turn everything in is 0.7000000 number of dielectric boundary points 37376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 15845 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) : 0.7427189 object centre at (A) : 1.392500 15.24400 20.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6710256E-03 -0.1381567 midg,1,midg; midg,igrid,midg -3.0574420E-02 -1.9911572E-02 1,midg,midg; igrid,midg,midg 4.8108422E-03 -5.9293127E-03 gauss-seidel spectral radius is 0.9989371 estimated iterations to convergence 243 setup time was (sec) 0.9900000 now iterating at: 11:10:45 rms-change max change #iterations 5.139766 241.9223 at 10iterations 2.615093 85.34512 at 20iterations 1.334377 39.26145 at 30iterations 0.6827056 18.94126 at 40iterations 0.3487242 10.46292 at 50iterations 0.1790377 5.052691 at 60iterations 9.1221064E-02 2.444237 at 70iterations 4.6723966E-02 1.528152 at 80iterations 2.3954298E-02 0.6325760 at 90iterations 1.2258215E-02 0.3444576 at 100iterations 6.2562614E-03 0.1985388 at 110iterations 3.2008258E-03 9.2647552E-02 at 120iterations finished qdiffx linear iterations at : 11:10:55 total time elapsed so far: 11.03000 # loops : 120 mean,max change (kT/e) : 3.2008258E-03 9.2647552E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 11:10:55 11.199u 0.443s 0:11.91 97.6% 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 11:10:55 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 = 2128 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: 3.342235 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): -21.55600 24.34100 ymin,ymax (A): -7.757000 38.24500 zmin,zma (A): -3.395000 44.53700 x,y,z range (A): 45.89700 46.00200 47.93200 scale (grids/A): 3.342235 object centre (A): 1.392500 15.24400 20.57100 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 86.19722 88.63847 90.08362 assigned negative charge : -324.1440 centred at (gu) : 86.55379 88.79224 91.01749 start vw surface at 0.1000000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 196114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19320 grid for indexing accessible points = 1.400000 m= 103798 mr = 141030 m= 43967 mr = 86160 m= 13787 mr = 36365 m= 3241 mr = 10962 m= 458 mr = 2436 m= 27 mr = 337 m= 0 mr = 3 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 4130 time to turn everything in is 2.210000 number of dielectric boundary points 84099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15912 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) : 2.228157 object centre at (A) : 1.392500 15.24400 20.57100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3485414E-02 -1.294884 midg,1,midg; midg,igrid,midg -0.2846031 -0.1141307 1,midg,midg; igrid,midg,midg 6.6090092E-02 -0.1518198 gauss-seidel spectral radius is 0.9993225 estimated iterations to convergence 303 setup time was (sec) 2.550000 now iterating at: 11:10:58 rms-change max change #iterations 11.06261 276.1023 at 10iterations 6.542763 145.6565 at 20iterations 3.871423 75.99873 at 30iterations 2.285661 37.46367 at 40iterations 1.348671 25.57688 at 50iterations 0.7946467 14.79284 at 60iterations 0.4676419 9.350739 at 70iterations 0.2758358 4.660942 at 80iterations 0.1624241 2.735766 at 90iterations 9.5531568E-02 1.532192 at 100iterations 5.6149319E-02 0.9620590 at 110iterations 3.3013709E-02 0.5498047 at 120iterations 1.9447865E-02 0.3005047 at 130iterations 1.1431654E-02 0.1837597 at 140iterations 6.7395666E-03 0.1208332 at 150iterations 3.9620744E-03 6.2290192E-02 at 160iterations 2.3297793E-03 4.1399002E-02 at 170iterations 1.3716397E-03 2.0936966E-02 at 180iterations finished qdiffx linear iterations at : 11:11:15 total time elapsed so far: 19.24000 # loops : 180 mean,max change (kT/e) : 1.3716397E-03 2.0936966E-02 energy calculations done at 19.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.40000 DelPhi exited at 11:11:16 19.402u 0.471s 0:20.19 98.4% 0+0k 0+0io 0pf+0w