Mon Oct 10 00:49:40 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 00:49:40 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIR 278 has a net charge of 0.5140 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: 0.6325740 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): -9.443000 38.82900 ymin,ymax (A): -53.81600 -4.067000 zmin,zma (A): -20.63800 35.64000 x,y,z range (A): 48.27200 49.74900 56.27800 scale (grids/A): 0.6325740 object centre (A): 14.69300 -28.94150 7.501001 number of atom coordinates read : 2594 total number of charged atoms : 2451 net assigned charge : 2.014014 assigned positive charge : 394.2270 centred at (gu) : 90.31905 89.78931 89.76354 assigned negative charge : -392.2137 centred at (gu) : 90.31516 89.81076 89.75740 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7041 nv = 96 ne = 84 npr = 51791 no. pairs analyzed = 51791 no. exposed pairs = 3491 no. arc points = 24261 no. surface atoms = 1187 nbur = 1407 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3713 m= 0 mr = 34 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2308 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8343 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8557462E-09 2.8051999E-09 midg,1,midg; midg,igrid,midg 4.6191757E-09 2.8468988E-10 1,midg,midg; igrid,midg,midg 1.8587875E-09 2.9217977E-09 gauss-seidel spectral radius is 0.9870611 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 00:49:41 rms-change max change #iterations 0.1423434 23.31745 at 10iterations 1.3673231E-02 2.188437 at 20iterations 1.3404809E-03 0.2078910 at 30iterations 1.3174331E-04 1.9340515E-02 at 40iterations 1.6082278E-05 2.2125244E-03 at 50iterations finished qdiffx linear iterations at : 00:49:44 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.6082278E-05 2.2125244E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 00:49:44 3.550u 0.159s 0:03.99 92.7% 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 00:49:44 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIR 278 has a net charge of 0.5140 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: 1.897722 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): -9.443000 38.82900 ymin,ymax (A): -53.81600 -4.067000 zmin,zma (A): -20.63800 35.64000 x,y,z range (A): 48.27200 49.74900 56.27800 scale (grids/A): 1.897722 object centre (A): 14.69300 -28.94150 7.501001 number of atom coordinates read : 2594 total number of charged atoms : 2451 net assigned charge : 2.014014 assigned positive charge : 394.2270 centred at (gu) : 90.95668 89.36742 89.28986 assigned negative charge : -392.2137 centred at (gu) : 90.94511 89.43233 89.27202 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24261 grid for indexing accessible points = 1.400000 m= 26660 mr = 51312 m= 4380 mr = 19107 m= 293 mr = 2778 m= 0 mr = 96 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.5900000 number of dielectric boundary points 34094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19296 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) : 0.6325740 object centre at (A) : 14.69300 -28.94150 7.501001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9515235E-02 5.1198304E-02 midg,1,midg; midg,igrid,midg 6.6079106E-04 -2.0447245E-02 1,midg,midg; igrid,midg,midg 1.1675721E-02 -6.0733329E-03 gauss-seidel spectral radius is 0.9986418 estimated iterations to convergence 215 setup time was (sec) 0.8900000 now iterating at: 00:49:45 rms-change max change #iterations 4.300539 164.6603 at 10iterations 2.023816 73.20094 at 20iterations 0.9568847 30.55599 at 30iterations 0.4482739 15.81833 at 40iterations 0.2101634 7.559587 at 50iterations 9.9192776E-02 3.177769 at 60iterations 4.6532162E-02 1.472890 at 70iterations 2.1842167E-02 0.6520863 at 80iterations 1.0258824E-02 0.3418617 at 90iterations 4.8322668E-03 0.1551018 at 100iterations 2.2658089E-03 7.1472108E-02 at 110iterations 1.0677631E-03 3.6235809E-02 at 120iterations finished qdiffx linear iterations at : 00:49:53 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 1.0677631E-03 3.6235809E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 00:49:53 8.181u 0.216s 0:08.84 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 Mon Oct 10 2011 at 00:49:53 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2594 !!! WARNING: HIR 278 has a net charge of 0.5140 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: 2.846583 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): -9.443000 38.82900 ymin,ymax (A): -53.81600 -4.067000 zmin,zma (A): -20.63800 35.64000 x,y,z range (A): 48.27200 49.74900 56.27800 scale (grids/A): 2.846583 object centre (A): 14.69300 -28.94150 7.501001 number of atom coordinates read : 2594 total number of charged atoms : 2451 net assigned charge : 2.014014 assigned positive charge : 394.2270 centred at (gu) : 91.43486 89.05099 88.93474 assigned negative charge : -392.2137 centred at (gu) : 91.41774 89.14850 88.90800 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24261 grid for indexing accessible points = 1.400000 m= 85918 mr = 124974 m= 31250 mr = 68794 m= 8035 mr = 24750 m= 1286 mr = 6088 m= 82 mr = 867 m= 0 mr = 29 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 181 time to turn everything in is 1.490000 number of dielectric boundary points 76905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19608 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) : 1.897722 object centre at (A) : 14.69300 -28.94150 7.501001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2327584 0.9893823 midg,1,midg; midg,igrid,midg 1.2503931E-02 -0.2754721 1,midg,midg; igrid,midg,midg 0.2288592 -6.0909592E-02 gauss-seidel spectral radius is 0.9992699 estimated iterations to convergence 292 setup time was (sec) 1.820000 now iterating at: 00:49:55 rms-change max change #iterations 10.18570 350.4929 at 10iterations 6.057894 134.0104 at 20iterations 3.568508 86.96675 at 30iterations 2.091152 42.12766 at 40iterations 1.223616 25.45224 at 50iterations 0.7102727 14.41212 at 60iterations 0.4129418 7.455105 at 70iterations 0.2388391 4.421763 at 80iterations 0.1384563 2.544449 at 90iterations 7.9897337E-02 1.407829 at 100iterations 4.6186186E-02 0.8650255 at 110iterations 2.6712557E-02 0.4987466 at 120iterations 1.5421671E-02 0.2889013 at 130iterations 8.8997530E-03 0.1632614 at 140iterations 5.1346393E-03 9.0408325E-02 at 150iterations 2.9568586E-03 5.7783604E-02 at 160iterations 1.7074804E-03 2.9800415E-02 at 170iterations 9.8583661E-04 1.7505646E-02 at 180iterations finished qdiffx linear iterations at : 00:50:07 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 9.8583661E-04 1.7505646E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 00:50:07 13.294u 0.225s 0:13.80 97.8% 0+0k 0+0io 0pf+0w