Mon Oct 10 16:04:46 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 Mon Oct 10 2011 at 16:04:46 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 890 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5491539 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): 7.344000 59.03000 ymin,ymax (A): -29.60600 34.20100 zmin,zma (A): -29.26800 35.55900 x,y,z range (A): 51.68600 63.80700 64.82700 scale (grids/A): 0.5491539 object centre (A): 33.18700 2.297501 3.145501 number of atom coordinates read : 4299 total number of charged atoms : 4202 net assigned charge : 5.606015 assigned positive charge : 652.1720 centred at (gu) : 89.84889 89.55841 88.62668 assigned negative charge : -646.5693 centred at (gu) : 89.85996 89.52501 88.64880 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8500 nv = 96 ne = 84 npr = 86035 no. pairs analyzed = 86035 no. exposed pairs = 5417 no. arc points = 36745 no. surface atoms = 1827 nbur = 2472 mkacc time = 0.1500000 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= 338 mr = 4589 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3000000 number of dielectric boundary points 4231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3696 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 11164 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8435842E-10 1.1190524E-10 midg,1,midg; midg,igrid,midg 2.8765315E-11 6.7619116E-10 1,midg,midg; igrid,midg,midg 5.3098914E-10 2.6218658E-10 gauss-seidel spectral radius is 0.9830012 estimated iterations to convergence 63 setup time was (sec) 0.4900000 now iterating at: 16:04:47 rms-change max change #iterations 9.1851197E-02 13.65779 at 10iterations 6.5974817E-03 0.9126053 at 20iterations 7.5760024E-04 0.1366329 at 30iterations 2.3684962E-04 3.5163879E-02 at 40iterations 9.7169963E-05 1.3523102E-02 at 50iterations finished qdiffx linear iterations at : 16:04:49 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 9.7169963E-05 1.3523102E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 16:04:50 3.488u 0.162s 0:04.00 91.0% 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 Mon Oct 10 2011 at 16:04:50 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 890 has a net charge of 1.4000 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: 1.647462 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): 7.344000 59.03000 ymin,ymax (A): -29.60600 34.20100 zmin,zma (A): -29.26800 35.55900 x,y,z range (A): 51.68600 63.80700 64.82700 scale (grids/A): 1.647462 object centre (A): 33.18700 2.297501 3.145501 number of atom coordinates read : 4299 total number of charged atoms : 4202 net assigned charge : 5.606015 assigned positive charge : 652.1720 centred at (gu) : 89.54520 88.67379 85.87868 assigned negative charge : -646.5693 centred at (gu) : 89.57945 88.57479 85.94589 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 94820 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36745 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30725 mr = 66794 m= 3382 mr = 21422 m= 88 mr = 1677 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 577 time to turn everything in is 0.4500000 number of dielectric boundary points 39113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 386 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 32229 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) : 0.5491539 object centre at (A) : 33.18700 2.297501 3.145501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7699139E-02 -4.9043698E-03 midg,1,midg; midg,igrid,midg 1.2824038E-02 8.9715403E-03 1,midg,midg; igrid,midg,midg 4.2847209E-03 -1.1194872E-03 gauss-seidel spectral radius is 0.9983563 estimated iterations to convergence 196 setup time was (sec) 0.6700000 now iterating at: 16:04:51 rms-change max change #iterations 4.212837 154.4166 at 10iterations 1.826712 65.53510 at 20iterations 0.7988257 22.66956 at 30iterations 0.3478401 10.39699 at 40iterations 0.1517424 4.636312 at 50iterations 6.6134170E-02 1.977176 at 60iterations 2.8965082E-02 0.8725042 at 70iterations 1.2685755E-02 0.3809171 at 80iterations 5.5751456E-03 0.1657751 at 90iterations 2.4988789E-03 7.8442991E-02 at 100iterations 1.1609064E-03 4.0710449E-02 at 110iterations 5.8537285E-04 1.8100142E-02 at 120iterations finished qdiffx linear iterations at : 16:04:58 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 5.8537285E-04 1.8100142E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 16:04:58 7.913u 0.229s 0:08.44 96.3% 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 Mon Oct 10 2011 at 16:04:58 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 !!! WARNING: GLM 136 has a net charge of -0.0940 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN8 890 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.471192 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): 7.344000 59.03000 ymin,ymax (A): -29.60600 34.20100 zmin,zma (A): -29.26800 35.55900 x,y,z range (A): 51.68600 63.80700 64.82700 scale (grids/A): 2.471192 object centre (A): 33.18700 2.297501 3.145501 number of atom coordinates read : 4299 total number of charged atoms : 4202 net assigned charge : 5.606015 assigned positive charge : 652.1720 centred at (gu) : 89.31750 88.01025 83.81763 assigned negative charge : -646.5693 centred at (gu) : 89.36911 87.86211 83.91872 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 220572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36745 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105356 mr = 163384 m= 31296 mr = 83918 m= 5363 mr = 23719 m= 374 mr = 3551 m= 6 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1957 time to turn everything in is 1.130000 number of dielectric boundary points 88247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 33584 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) : 1.647462 object centre at (A) : 33.18700 2.297501 3.145501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4312209 -0.1096854 midg,1,midg; midg,igrid,midg 0.3206676 9.9130005E-02 1,midg,midg; igrid,midg,midg 5.2951898E-02 -6.2079467E-03 gauss-seidel spectral radius is 0.9992262 estimated iterations to convergence 284 setup time was (sec) 1.370000 now iterating at: 16:05:00 rms-change max change #iterations 10.88465 304.3109 at 10iterations 6.387796 158.0328 at 20iterations 3.724211 92.86670 at 30iterations 2.161165 42.66415 at 40iterations 1.247935 23.40680 at 50iterations 0.7185548 13.21388 at 60iterations 0.4120269 7.535106 at 70iterations 0.2365198 4.262257 at 80iterations 0.1355182 2.387516 at 90iterations 7.7575818E-02 1.357944 at 100iterations 4.4337761E-02 0.7621002 at 110iterations 2.5302008E-02 0.4449625 at 120iterations 1.4439320E-02 0.2439375 at 130iterations 8.2835471E-03 0.1535645 at 140iterations 4.7532693E-03 8.6292267E-02 at 150iterations 2.7469052E-03 4.7454834E-02 at 160iterations 1.6132966E-03 3.2718658E-02 at 170iterations 9.7258715E-04 1.7341614E-02 at 180iterations finished qdiffx linear iterations at : 16:05:12 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 9.7258715E-04 1.7341614E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.08000 DelPhi exited at 16:05:12 13.085u 0.223s 0:13.80 96.3% 0+0k 0+0io 0pf+0w