Sat Oct 8 22:54:00 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 Sat Oct 8 2011 at 22:54:00 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5740639 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): -15.88300 40.39700 ymin,ymax (A): 16.61100 76.28500 zmin,zma (A): 25.72000 87.73400 x,y,z range (A): 56.28000 59.67400 62.01400 scale (grids/A): 0.5740639 object centre (A): 12.25700 46.44800 56.72700 number of atom coordinates read : 3266 total number of charged atoms : 3122 net assigned charge : 14.87703 assigned positive charge : 483.7647 centred at (gu) : 89.84441 89.97150 90.60210 assigned negative charge : -468.8894 centred at (gu) : 89.71364 89.99948 90.83074 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7345 nv = 96 ne = 84 npr = 64318 no. pairs analyzed = 64318 no. exposed pairs = 4200 no. arc points = 30612 no. surface atoms = 1400 nbur = 1866 mkacc time = 0.2100000 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 = 1.484000 m= 342 mr = 3807 m= 4 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.4800000 number of dielectric boundary points 3851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3071 ## 368 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9281 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0019345E-09 -2.0974984E-09 midg,1,midg; midg,igrid,midg 3.2324021E-09 2.1320585E-09 1,midg,midg; igrid,midg,midg 1.5230157E-10 4.9469455E-09 gauss-seidel spectral radius is 0.9843755 estimated iterations to convergence 66 setup time was (sec) 0.7800000 now iterating at: 22:54:01 rms-change max change #iterations 0.1008098 15.81362 at 10iterations 7.6521211E-03 1.213870 at 20iterations 6.0206628E-04 9.4767570E-02 at 30iterations 5.3217158E-05 8.2931519E-03 at 40iterations 6.3605275E-06 7.4005127E-04 at 50iterations finished qdiffx linear iterations at : 22:54:05 total time elapsed so far: 4.740000 # loops : 50 mean,max change (kT/e) : 6.3605275E-06 7.4005127E-04 energy calculations done at 4.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.960000 DelPhi exited at 22:54:06 4.963u 0.466s 0:05.70 95.0% 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 Sat Oct 8 2011 at 22:54:06 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.722192 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): -15.88300 40.39700 ymin,ymax (A): 16.61100 76.28500 zmin,zma (A): 25.72000 87.73400 x,y,z range (A): 56.28000 59.67400 62.01400 scale (grids/A): 1.722192 object centre (A): 12.25700 46.44800 56.72700 number of atom coordinates read : 3266 total number of charged atoms : 3122 net assigned charge : 14.87703 assigned positive charge : 483.7647 centred at (gu) : 89.53204 89.91366 91.80527 assigned negative charge : -468.8894 centred at (gu) : 89.14061 89.99828 92.49230 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 80546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30612 grid for indexing accessible points = 1.400000 m= 25659 mr = 54278 m= 3168 mr = 18008 m= 143 mr = 1780 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2100 time to turn everything in is 0.8300000 number of dielectric boundary points 35421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 24219 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) : 0.5740639 object centre at (A) : 12.25700 46.44800 56.72700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1567581E-02 7.6633841E-03 midg,1,midg; midg,igrid,midg 4.0281564E-02 1.5310086E-02 1,midg,midg; igrid,midg,midg -7.3046121E-03 1.4199830E-02 gauss-seidel spectral radius is 0.9984193 estimated iterations to convergence 200 setup time was (sec) 1.170000 now iterating at: 22:54:08 rms-change max change #iterations 3.884450 163.6931 at 10iterations 1.706932 59.42374 at 20iterations 0.7525408 25.02864 at 30iterations 0.3317771 11.20181 at 40iterations 0.1460626 5.207434 at 50iterations 6.4568654E-02 2.023266 at 60iterations 2.8533839E-02 0.9100992 at 70iterations 1.2658985E-02 0.4040775 at 80iterations 5.5891881E-03 0.1925898 at 90iterations 2.4649606E-03 7.8493118E-02 at 100iterations 1.0938057E-03 3.2546997E-02 at 110iterations 4.8170806E-04 1.5382767E-02 at 120iterations finished qdiffx linear iterations at : 22:54:18 total time elapsed so far: 11.45000 # loops : 120 mean,max change (kT/e) : 4.8170806E-04 1.5382767E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 22:54:18 11.670u 0.500s 0:12.50 97.3% 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 Sat Oct 8 2011 at 22:54:19 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3266 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.583288 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): -15.88300 40.39700 ymin,ymax (A): 16.61100 76.28500 zmin,zma (A): 25.72000 87.73400 x,y,z range (A): 56.28000 59.67400 62.01400 scale (grids/A): 2.583288 object centre (A): 12.25700 46.44800 56.72700 number of atom coordinates read : 3266 total number of charged atoms : 3122 net assigned charge : 14.87703 assigned positive charge : 483.7647 centred at (gu) : 89.29781 89.87039 92.70776 assigned negative charge : -468.8894 centred at (gu) : 88.71084 89.99730 93.73838 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 187192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30612 grid for indexing accessible points = 1.400000 m= 87170 mr = 133309 m= 26889 mr = 69053 m= 5228 mr = 20710 m= 567 mr = 3672 m= 12 mr = 350 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 7157 time to turn everything in is 2.050000 number of dielectric boundary points 79964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 24953 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) : 1.722192 object centre at (A) : 12.25700 46.44800 56.72700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7054371 8.9269623E-02 midg,1,midg; midg,igrid,midg 0.6393604 0.2990929 1,midg,midg; igrid,midg,midg -6.3687742E-02 0.1996590 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 2.450000 now iterating at: 22:54:21 rms-change max change #iterations 9.735620 310.6556 at 10iterations 5.655219 143.1859 at 20iterations 3.261277 76.16917 at 30iterations 1.867637 41.23569 at 40iterations 1.069882 22.97624 at 50iterations 0.6100403 11.43066 at 60iterations 0.3478693 7.057129 at 70iterations 0.1981869 4.143841 at 80iterations 0.1127137 2.280507 at 90iterations 6.4073734E-02 1.172535 at 100iterations 3.6303304E-02 0.6641655 at 110iterations 2.0565080E-02 0.4338493 at 120iterations 1.1677470E-02 0.2151623 at 130iterations 6.6209063E-03 0.1182747 at 140iterations 3.7464821E-03 7.1618080E-02 at 150iterations 2.1221524E-03 3.9718628E-02 at 160iterations 1.2020232E-03 2.2034168E-02 at 170iterations 6.8074319E-04 1.4427185E-02 at 180iterations finished qdiffx linear iterations at : 22:54:40 total time elapsed so far: 20.78000 # loops : 180 mean,max change (kT/e) : 6.8074319E-04 1.4427185E-02 energy calculations done at 20.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.01000 DelPhi exited at 22:54:40 21.013u 0.529s 0:21.88 98.4% 0+0k 0+0io 0pf+0w