Sun Oct 9 11:54:22 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 Sun Oct 9 2011 at 11:54:22 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 = 2648 !!! WARNING: VAL 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6633375 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): 51.41600 104.0460 ymin,ymax (A): 5.389000 58.17500 zmin,zma (A): 34.44000 88.10800 x,y,z range (A): 52.63000 52.78600 53.66800 scale (grids/A): 0.6633375 object centre (A): 77.73100 31.78200 61.27400 number of atom coordinates read : 2648 total number of charged atoms : 2576 net assigned charge : 0.2280082 assigned positive charge : 387.9152 centred at (gu) : 89.31328 89.41550 92.77228 assigned negative charge : -387.6888 centred at (gu) : 89.49529 89.49474 92.69895 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8573 nv = 96 ne = 84 npr = 50110 no. pairs analyzed = 50110 no. exposed pairs = 3761 no. arc points = 26921 no. surface atoms = 1261 nbur = 1387 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 589 mr = 4432 m= 3 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3300000 number of dielectric boundary points 4638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9701 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.9720631E-09 2.7744493E-08 midg,1,midg; midg,igrid,midg 1.8724617E-08 -1.5264099E-08 1,midg,midg; igrid,midg,midg 4.3809390E-08 -3.4443097E-08 gauss-seidel spectral radius is 0.9882511 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 11:54:22 rms-change max change #iterations 0.1702013 24.41731 at 10iterations 1.8351551E-02 2.491514 at 20iterations 2.0942432E-03 0.2841835 at 30iterations 3.4630520E-04 5.8181763E-02 at 40iterations 9.7808232E-05 1.8302917E-02 at 50iterations finished qdiffx linear iterations at : 11:54:25 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 9.7808232E-05 1.8302917E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 11:54:26 3.417u 0.158s 0:03.87 91.9% 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 Sun Oct 9 2011 at 11:54:26 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 = 2648 !!! WARNING: VAL 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.990013 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): 51.41600 104.0460 ymin,ymax (A): 5.389000 58.17500 zmin,zma (A): 34.44000 88.10800 x,y,z range (A): 52.63000 52.78600 53.66800 scale (grids/A): 1.990013 object centre (A): 77.73100 31.78200 61.27400 number of atom coordinates read : 2648 total number of charged atoms : 2576 net assigned charge : 0.2280082 assigned positive charge : 387.9152 centred at (gu) : 87.93902 88.24580 98.31631 assigned negative charge : -387.6888 centred at (gu) : 88.48583 88.48395 98.09676 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 90244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26921 grid for indexing accessible points = 1.400000 m= 35313 mr = 60207 m= 7546 mr = 25594 m= 638 mr = 4941 m= 10 mr = 300 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 42709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20387 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) : 0.6633375 object centre at (A) : 77.73100 31.78200 61.27400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3782774E-02 7.5716138E-02 midg,1,midg; midg,igrid,midg 2.1311831E-02 4.6064244E-03 1,midg,midg; igrid,midg,midg 3.1095587E-02 -4.5602892E-02 gauss-seidel spectral radius is 0.9987845 estimated iterations to convergence 227 setup time was (sec) 0.9600000 now iterating at: 11:54:27 rms-change max change #iterations 4.669798 189.5468 at 10iterations 2.288859 69.83308 at 20iterations 1.116004 33.01134 at 30iterations 0.5458293 16.53038 at 40iterations 0.2674427 8.171803 at 50iterations 0.1309106 4.009747 at 60iterations 6.3820221E-02 2.202332 at 70iterations 3.1301789E-02 1.012043 at 80iterations 1.5319890E-02 0.4549470 at 90iterations 7.5123855E-03 0.2156563 at 100iterations 3.7006573E-03 0.1088230 at 110iterations 1.8228131E-03 5.6011677E-02 at 120iterations finished qdiffx linear iterations at : 11:54:33 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.8228131E-03 5.6011677E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 11:54:34 7.820u 0.192s 0:08.44 94.9% 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 Sun Oct 9 2011 at 11:54:34 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 = 2648 !!! WARNING: VAL 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.985019 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): 51.41600 104.0460 ymin,ymax (A): 5.389000 58.17500 zmin,zma (A): 34.44000 88.10800 x,y,z range (A): 52.63000 52.78600 53.66800 scale (grids/A): 2.985019 object centre (A): 77.73100 31.78200 61.27400 number of atom coordinates read : 2648 total number of charged atoms : 2576 net assigned charge : 0.2280082 assigned positive charge : 387.9152 centred at (gu) : 86.90844 87.36838 102.4744 assigned negative charge : -387.6888 centred at (gu) : 87.72865 87.72601 102.1451 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 207925 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26921 grid for indexing accessible points = 1.400000 m= 108066 mr = 146316 m= 45918 mr = 86586 m= 14269 mr = 36728 m= 2716 mr = 11025 m= 230 mr = 1949 m= 1 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 96417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 20607 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) : 1.990013 object centre at (A) : 77.73100 31.78200 61.27400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1257777 0.9471752 midg,1,midg; midg,igrid,midg 0.2113600 -0.1305548 1,midg,midg; igrid,midg,midg 0.2172667 -0.4272304 gauss-seidel spectral radius is 0.9993271 estimated iterations to convergence 304 setup time was (sec) 2.080000 now iterating at: 11:54:36 rms-change max change #iterations 10.95512 370.5359 at 10iterations 6.650689 133.8882 at 20iterations 4.005713 98.61674 at 30iterations 2.402658 47.69663 at 40iterations 1.438805 29.23254 at 50iterations 0.8573758 15.02922 at 60iterations 0.5107993 9.308521 at 70iterations 0.3035959 5.247587 at 80iterations 0.1802119 3.160742 at 90iterations 0.1066964 1.847523 at 100iterations 6.3301630E-02 1.125438 at 110iterations 3.7448362E-02 0.6481171 at 120iterations 2.2150051E-02 0.3628235 at 130iterations 1.3105530E-02 0.2174792 at 140iterations 7.7473307E-03 0.1283722 at 150iterations 4.6193413E-03 8.5132122E-02 at 160iterations 2.7501974E-03 4.7151566E-02 at 170iterations 1.6592436E-03 3.2249451E-02 at 180iterations finished qdiffx linear iterations at : 11:54:47 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 1.6592436E-03 3.2249451E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 11:54:48 13.060u 0.184s 0:13.52 97.9% 0+0k 0+0io 0pf+0w