Mon Oct 10 17:15:57 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 17:15:57 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 = 2914 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: 0.5518097 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): -2.518000 61.99700 ymin,ymax (A): 12.05600 58.61900 zmin,zma (A): -7.590000 39.58600 x,y,z range (A): 64.51500 46.56300 47.17600 scale (grids/A): 0.5518097 object centre (A): 29.73950 35.33750 15.99800 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -4.499961 assigned positive charge : 433.9630 centred at (gu) : 89.76749 89.68761 89.29272 assigned negative charge : -438.4641 centred at (gu) : 89.68221 89.85989 89.25916 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5626 nv = 96 ne = 84 npr = 59449 no. pairs analyzed = 59449 no. exposed pairs = 3765 no. arc points = 26164 no. surface atoms = 1287 nbur = 1627 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 = 1.568000 m= 200 mr = 2785 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2100000 number of dielectric boundary points 3038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2660 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7350 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4217393E-10 -6.8378261E-11 midg,1,midg; midg,igrid,midg 1.1052289E-09 -1.6498859E-09 1,midg,midg; igrid,midg,midg -1.1134133E-09 3.1606015E-10 gauss-seidel spectral radius is 0.9830585 estimated iterations to convergence 63 setup time was (sec) 0.4100000 now iterating at: 17:15:58 rms-change max change #iterations 7.5677678E-02 12.29342 at 10iterations 5.2541075E-03 0.8640289 at 20iterations 3.5320234E-04 6.0289860E-02 at 30iterations 2.4016683E-05 4.4422150E-03 at 40iterations 1.6320058E-06 2.6249886E-04 at 50iterations finished qdiffx linear iterations at : 17:16:01 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.6320058E-06 2.6249886E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:16:01 3.432u 0.173s 0:03.93 91.6% 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 17:16:01 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 = 2914 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: 1.655429 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): -2.518000 61.99700 ymin,ymax (A): 12.05600 58.61900 zmin,zma (A): -7.590000 39.58600 x,y,z range (A): 64.51500 46.56300 47.17600 scale (grids/A): 1.655429 object centre (A): 29.73950 35.33750 15.99800 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -4.499961 assigned positive charge : 433.9630 centred at (gu) : 89.30148 89.06208 87.87701 assigned negative charge : -438.4641 centred at (gu) : 89.04648 89.57919 87.77718 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26164 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18070 mr = 40840 m= 1765 mr = 12064 m= 43 mr = 789 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 996 time to turn everything in is 0.3100000 number of dielectric boundary points 28017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 300 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 21290 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) : 0.5518097 object centre at (A) : 29.73950 35.33750 15.99800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1744257E-03 -1.5319595E-03 midg,1,midg; midg,igrid,midg 9.5549077E-03 -1.8950317E-02 1,midg,midg; igrid,midg,midg -2.9096683E-02 -6.9408645E-03 gauss-seidel spectral radius is 0.9982226 estimated iterations to convergence 188 setup time was (sec) 0.5200000 now iterating at: 17:16:02 rms-change max change #iterations 3.374844 191.1038 at 10iterations 1.403040 56.11705 at 20iterations 0.5893235 23.40030 at 30iterations 0.2479556 9.793236 at 40iterations 0.1042436 3.641132 at 50iterations 4.3952055E-02 1.680511 at 60iterations 1.8453564E-02 0.7871532 at 70iterations 7.7567799E-03 0.2966490 at 80iterations 3.2729844E-03 0.1172857 at 90iterations 1.3652837E-03 5.0745010E-02 at 100iterations 5.7993381E-04 2.3777008E-02 at 110iterations 2.4308110E-04 8.8320971E-03 at 120iterations finished qdiffx linear iterations at : 17:16:09 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 2.4308110E-04 8.8320971E-03 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 17:16:09 7.591u 0.190s 0:08.06 96.5% 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 17:16:09 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 = 2914 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: 2.483144 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): -2.518000 61.99700 ymin,ymax (A): 12.05600 58.61900 zmin,zma (A): -7.590000 39.58600 x,y,z range (A): 64.51500 46.56300 47.17600 scale (grids/A): 2.483144 object centre (A): 29.73950 35.33750 15.99800 number of atom coordinates read : 2914 total number of charged atoms : 2773 net assigned charge : -4.499961 assigned positive charge : 433.9630 centred at (gu) : 88.95204 88.59293 86.81529 assigned negative charge : -438.4641 centred at (gu) : 88.56956 89.36880 86.66570 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 143688 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26164 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 63288 mr = 100334 m= 17255 mr = 49237 m= 2589 mr = 12581 m= 192 mr = 1583 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 3161 time to turn everything in is 0.7400000 number of dielectric boundary points 63192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22158 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) : 1.655429 object centre at (A) : 29.73950 35.33750 15.99800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8278321E-02 -2.3589220E-02 midg,1,midg; midg,igrid,midg 0.1519048 -0.2525037 1,midg,midg; igrid,midg,midg -0.8248695 -7.9022907E-02 gauss-seidel spectral radius is 0.9991511 estimated iterations to convergence 271 setup time was (sec) 0.9700000 now iterating at: 17:16:11 rms-change max change #iterations 8.722559 340.3849 at 10iterations 4.890331 141.7235 at 20iterations 2.729057 69.54750 at 30iterations 1.517777 36.65105 at 40iterations 0.8429694 21.95923 at 50iterations 0.4672447 10.02206 at 60iterations 0.2585745 5.615376 at 70iterations 0.1428818 2.942497 at 80iterations 7.8677796E-02 1.946827 at 90iterations 4.3492794E-02 0.9307076 at 100iterations 2.4055675E-02 0.5013199 at 110iterations 1.3253771E-02 0.2823019 at 120iterations 7.2954637E-03 0.1507378 at 130iterations 4.0318514E-03 9.2144251E-02 at 140iterations 2.2159123E-03 4.9568892E-02 at 150iterations 1.2217110E-03 2.5499344E-02 at 160iterations 6.7450415E-04 1.4593124E-02 at 170iterations 3.7115821E-04 7.1668625E-03 at 180iterations finished qdiffx linear iterations at : 17:16:22 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 3.7115821E-04 7.1668625E-03 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 17:16:22 12.053u 0.202s 0:12.81 95.6% 0+0k 0+0io 0pf+0w