Tue Oct 11 05:48:49 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 Tue Oct 11 2011 at 05:48:50 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 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: 0.7193372 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): 3.519000 47.79200 ymin,ymax (A): 1.785000 39.30300 zmin,zma (A): -2.754000 46.73600 x,y,z range (A): 44.27300 37.51800 49.49000 scale (grids/A): 0.7193372 object centre (A): 25.65550 20.54400 21.99100 number of atom coordinates read : 2232 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 89.73212 90.78388 90.56655 assigned negative charge : -303.7472 centred at (gu) : 89.92334 90.77981 90.58833 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7199 nv = 96 ne = 84 npr = 41686 no. pairs analyzed = 41686 no. exposed pairs = 2474 no. arc points = 16739 no. surface atoms = 841 nbur = 1391 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4188 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1499 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7884 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7118728E-08 7.7203538E-08 midg,1,midg; midg,igrid,midg 6.9859567E-08 9.9244964E-08 1,midg,midg; igrid,midg,midg 2.1104856E-07 -3.6275186E-08 gauss-seidel spectral radius is 0.9899188 estimated iterations to convergence 81 setup time was (sec) 0.3700000 now iterating at: 05:48:50 rms-change max change #iterations 0.2093043 29.70105 at 10iterations 2.7006416E-02 3.997240 at 20iterations 3.5736663E-03 0.4870300 at 30iterations 5.7342940E-04 7.9162598E-02 at 40iterations 1.2551286E-04 1.5762329E-02 at 50iterations finished qdiffx linear iterations at : 05:48:53 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.2551286E-04 1.5762329E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 05:48:53 3.434u 0.154s 0:03.96 90.4% 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 Tue Oct 11 2011 at 05:48:54 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 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: 2.158012 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): 3.519000 47.79200 ymin,ymax (A): 1.785000 39.30300 zmin,zma (A): -2.754000 46.73600 x,y,z range (A): 44.27300 37.51800 49.49000 scale (grids/A): 2.158012 object centre (A): 25.65550 20.54400 21.99100 number of atom coordinates read : 2232 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 89.19637 92.35167 91.69969 assigned negative charge : -303.7472 centred at (gu) : 89.77002 92.33967 91.76512 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16739 grid for indexing accessible points = 1.400000 m= 30666 mr = 54485 m= 6116 mr = 23431 m= 652 mr = 4177 m= 12 mr = 350 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15241 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) : 0.7193372 object centre at (A) : 25.65550 20.54400 21.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0989865E-02 7.8270249E-02 midg,1,midg; midg,igrid,midg 7.6578865E-03 3.6593262E-02 1,midg,midg; igrid,midg,midg 5.4186687E-02 5.7217637E-03 gauss-seidel spectral radius is 0.9988592 estimated iterations to convergence 234 setup time was (sec) 0.6200000 now iterating at: 05:48:54 rms-change max change #iterations 4.674530 244.2365 at 10iterations 2.333464 70.67018 at 20iterations 1.170824 40.49043 at 30iterations 0.5849465 17.06474 at 40iterations 0.2942555 9.226256 at 50iterations 0.1473248 4.441512 at 60iterations 7.3901579E-02 2.080505 at 70iterations 3.7057765E-02 1.150648 at 80iterations 1.8621726E-02 0.5775833 at 90iterations 9.3925614E-03 0.2970695 at 100iterations 4.7417926E-03 0.1446657 at 110iterations 2.4358111E-03 7.3807716E-02 at 120iterations finished qdiffx linear iterations at : 05:49:02 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.4358111E-03 7.3807716E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 05:49:02 7.947u 0.194s 0:08.46 96.0% 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 Tue Oct 11 2011 at 05:49:02 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 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: 3.237017 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): 3.519000 47.79200 ymin,ymax (A): 1.785000 39.30300 zmin,zma (A): -2.754000 46.73600 x,y,z range (A): 44.27300 37.51800 49.49000 scale (grids/A): 3.237017 object centre (A): 25.65550 20.54400 21.99100 number of atom coordinates read : 2232 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.2470 centred at (gu) : 88.79461 93.52747 92.54946 assigned negative charge : -303.7472 centred at (gu) : 89.65509 93.50956 92.64772 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16739 grid for indexing accessible points = 1.400000 m= 95760 mr = 131290 m= 38999 mr = 80010 m= 11545 mr = 32152 m= 2459 mr = 8991 m= 301 mr = 1844 m= 7 mr = 210 m= 0 mr = 2 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 15427 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) : 2.158012 object centre at (A) : 25.65550 20.54400 21.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3211402 0.7230654 midg,1,midg; midg,igrid,midg 2.8550560E-02 0.2770979 1,midg,midg; igrid,midg,midg 0.4237372 0.1412371 gauss-seidel spectral radius is 0.9992999 estimated iterations to convergence 298 setup time was (sec) 1.430000 now iterating at: 05:49:04 rms-change max change #iterations 10.34402 329.1646 at 10iterations 6.122358 130.2762 at 20iterations 3.625795 76.92087 at 30iterations 2.140278 41.86610 at 40iterations 1.262272 22.15875 at 50iterations 0.7412697 13.31178 at 60iterations 0.4368890 8.082211 at 70iterations 0.2563193 4.587881 at 80iterations 0.1506535 2.798990 at 90iterations 8.8587686E-02 1.726017 at 100iterations 5.2118056E-02 0.9271650 at 110iterations 3.0688941E-02 0.5469280 at 120iterations 1.8254682E-02 0.3615303 at 130iterations 1.0954291E-02 0.2073879 at 140iterations 6.7429170E-03 0.1179161 at 150iterations 4.2955088E-03 7.6923370E-02 at 160iterations 2.8660393E-03 5.1273346E-02 at 170iterations 2.0333095E-03 3.2604218E-02 at 180iterations finished qdiffx linear iterations at : 05:49:15 total time elapsed so far: 12.75000 # loops : 180 mean,max change (kT/e) : 2.0333095E-03 3.2604218E-02 energy calculations done at 12.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 05:49:15 12.884u 0.207s 0:13.39 97.6% 0+0k 0+0io 0pf+0w