Wed Feb 15 08:55:17 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 08:55:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 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: 0.5585365 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 0.5585365 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.00003 assigned positive charge : 411.4209 centred at (gu) : 92.19225 91.43732 86.75813 assigned negative charge : -401.4214 centred at (gu) : 92.26601 91.45894 86.54906 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5873 nv = 96 ne = 84 npr = 56281 no. pairs analyzed = 56281 no. exposed pairs = 4232 no. arc points = 30829 no. surface atoms = 1405 nbur = 1422 mkacc time = 0.1000000 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 = 1.540000 m= 246 mr = 2490 m= 0 mr = 9 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3063 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7546 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1435411E-09 1.3717739E-09 midg,1,midg; midg,igrid,midg 9.1096702E-10 1.2306172E-09 1,midg,midg; igrid,midg,midg 1.0443778E-09 6.2838357E-10 gauss-seidel spectral radius is 0.9834694 estimated iterations to convergence 64 setup time was (sec) 0.4300000 now iterating at: 08:55:18 rms-change max change #iterations 7.5561799E-02 13.73994 at 10iterations 5.3635850E-03 1.013023 at 20iterations 3.9010652E-04 6.7646027E-02 at 30iterations 3.8433442E-05 8.0556870E-03 at 40iterations 6.2453337E-06 7.6532364E-04 at 50iterations finished qdiffx linear iterations at : 08:55:21 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 6.2453337E-06 7.6532364E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 08:55:21 3.505u 0.235s 0:07.33 50.8% 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 Wed Feb 15 2012 at 08:55:25 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 = 2827 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: 1.675610 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 1.675610 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.00003 assigned positive charge : 411.4209 centred at (gu) : 96.57615 94.31160 80.27397 assigned negative charge : -401.4214 centred at (gu) : 96.79787 94.37658 79.64693 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30829 grid for indexing accessible points = 1.400000 m= 19178 mr = 38144 m= 2130 mr = 11954 m= 60 mr = 898 m= 0 mr = 4 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 33484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 20586 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) : 0.5585365 object centre at (A) : 9.274999 16.02550 24.95600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9274814E-03 1.1584891E-02 midg,1,midg; midg,igrid,midg 1.5950054E-02 2.2894591E-02 1,midg,midg; igrid,midg,midg -9.7947819E-03 -1.1763829E-02 gauss-seidel spectral radius is 0.9982718 estimated iterations to convergence 191 setup time was (sec) 0.5400000 now iterating at: 08:55:25 rms-change max change #iterations 3.302839 141.6802 at 10iterations 1.396826 59.53615 at 20iterations 0.5902877 21.72820 at 30iterations 0.2509556 10.10951 at 40iterations 0.1062453 3.789709 at 50iterations 4.4956863E-02 1.654305 at 60iterations 1.9061189E-02 0.7338629 at 70iterations 8.1041111E-03 0.3249817 at 80iterations 3.4476290E-03 0.1249323 at 90iterations 1.4624262E-03 5.5166245E-02 at 100iterations 6.2129775E-04 2.2716522E-02 at 110iterations 2.6630479E-04 9.1266632E-03 at 120iterations finished qdiffx linear iterations at : 08:55:32 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.6630479E-04 9.1266632E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 08:55:33 7.757u 0.201s 0:08.46 93.9% 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 Wed Feb 15 2012 at 08:55:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2827 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: 2.513414 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): -22.59400 41.14400 ymin,ymax (A): -12.28900 44.34000 zmin,zma (A): -1.947000 51.85900 x,y,z range (A): 63.73800 56.62900 53.80600 scale (grids/A): 2.513414 object centre (A): 9.274999 16.02550 24.95600 number of atom coordinates read : 2827 total number of charged atoms : 2678 net assigned charge : 10.00003 assigned positive charge : 411.4209 centred at (gu) : 99.86421 96.46729 75.41088 assigned negative charge : -401.4214 centred at (gu) : 100.1968 96.56484 74.47036 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 145998 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30829 grid for indexing accessible points = 1.400000 m= 64153 mr = 94450 m= 19266 mr = 47432 m= 3233 mr = 13500 m= 233 mr = 1857 m= 6 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 75556 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 21416 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) : 1.675610 object centre at (A) : 9.274999 16.02550 24.95600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.3275988E-03 0.1332061 midg,1,midg; midg,igrid,midg 0.3063022 0.2813187 1,midg,midg; igrid,midg,midg -0.3320461 -0.3684435 gauss-seidel spectral radius is 0.9991689 estimated iterations to convergence 274 setup time was (sec) 1.020000 now iterating at: 08:55:34 rms-change max change #iterations 8.858910 349.1252 at 10iterations 5.173134 179.7780 at 20iterations 2.963992 84.97808 at 30iterations 1.685032 48.69016 at 40iterations 0.9531974 31.06385 at 50iterations 0.5367255 13.26357 at 60iterations 0.3013313 7.623972 at 70iterations 0.1690861 4.205654 at 80iterations 9.4546393E-02 2.221634 at 90iterations 5.2791484E-02 1.249142 at 100iterations 2.9402874E-02 0.7219543 at 110iterations 1.6403828E-02 0.3807373 at 120iterations 9.1320658E-03 0.2031517 at 130iterations 5.0769136E-03 0.1127291 at 140iterations 2.8277398E-03 6.2118530E-02 at 150iterations 1.5723866E-03 3.7348747E-02 at 160iterations 8.7259646E-04 1.8141270E-02 at 170iterations 4.8606240E-04 1.0772705E-02 at 180iterations finished qdiffx linear iterations at : 08:55:46 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 4.8606240E-04 1.0772705E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 08:55:47 12.447u 0.199s 0:13.37 94.4% 0+0k 0+0io 0pf+0w