Sun Oct 9 18:06:33 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 18:06:33 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5195 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5505807 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): 3.295000 67.95400 ymin,ymax (A): -8.667000 53.21800 zmin,zma (A): -1.247000 61.41900 x,y,z range (A): 64.65900 61.88500 62.66600 scale (grids/A): 0.5505807 object centre (A): 35.62450 22.27550 30.08600 number of atom coordinates read : 5195 total number of charged atoms : 5043 net assigned charge : -0.3789458 assigned positive charge : 796.4135 centred at (gu) : 87.79478 89.25215 89.39745 assigned negative charge : -796.7986 centred at (gu) : 87.67469 89.28902 89.35281 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 10134 nv = 96 ne = 84 npr = 106300 no. pairs analyzed = 106300 no. exposed pairs = 6006 no. arc points = 40831 no. surface atoms = 2044 nbur = 3151 mkacc time = 0.1900000 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 = 1.540000 m= 434 mr = 5772 m= 0 mr = 23 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4177 ## 478 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 13448 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.1459533E-10 5.4784488E-10 midg,1,midg; midg,igrid,midg 6.3841699E-10 -4.1910622E-10 1,midg,midg; igrid,midg,midg -2.9622320E-09 9.7116959E-10 gauss-seidel spectral radius is 0.9831461 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 18:06:33 rms-change max change #iterations 0.1067414 14.11158 at 10iterations 9.8561356E-03 1.220078 at 20iterations 2.7695934E-03 0.3030624 at 30iterations 1.2013005E-03 0.1433803 at 40iterations 5.4124533E-04 6.7708850E-02 at 50iterations finished qdiffx linear iterations at : 18:06:36 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 5.4124533E-04 6.7708850E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 18:06:37 3.629u 0.149s 0:04.08 92.1% 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 18:06:37 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5195 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.651742 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): 3.295000 67.95400 ymin,ymax (A): -8.667000 53.21800 zmin,zma (A): -1.247000 61.41900 x,y,z range (A): 64.65900 61.88500 62.66600 scale (grids/A): 1.651742 object centre (A): 35.62450 22.27550 30.08600 number of atom coordinates read : 5195 total number of charged atoms : 5043 net assigned charge : -0.3789458 assigned positive charge : 796.4135 centred at (gu) : 83.38268 87.75476 88.19054 assigned negative charge : -796.7986 centred at (gu) : 83.02403 87.86708 88.05837 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 113440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40831 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38291 mr = 82264 m= 4455 mr = 27567 m= 140 mr = 2322 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 270 time to turn everything in is 0.5400000 number of dielectric boundary points 44155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 38699 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) : 0.5505807 object centre at (A) : 35.62450 22.27550 30.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4879623E-02 -1.4809431E-02 midg,1,midg; midg,igrid,midg 1.8473977E-02 6.9851703E-03 1,midg,midg; igrid,midg,midg -2.7976917E-02 1.3737131E-02 gauss-seidel spectral radius is 0.9984228 estimated iterations to convergence 200 setup time was (sec) 0.7700000 now iterating at: 18:06:38 rms-change max change #iterations 4.809263 204.8476 at 10iterations 2.121206 59.98355 at 20iterations 0.9438220 29.36768 at 30iterations 0.4184376 13.36133 at 40iterations 0.1858494 4.966156 at 50iterations 8.2723394E-02 2.363246 at 60iterations 3.7188191E-02 1.036560 at 70iterations 1.7075900E-02 0.5051070 at 80iterations 8.2971295E-03 0.2539291 at 90iterations 4.4393423E-03 0.1168289 at 100iterations 2.7143627E-03 7.3427200E-02 at 110iterations 1.8570939E-03 4.6352386E-02 at 120iterations finished qdiffx linear iterations at : 18:06:45 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 1.8570939E-03 4.6352386E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 18:06:46 8.227u 0.203s 0:08.74 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 Sun Oct 9 2011 at 18:06:46 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5195 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.477613 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): 3.295000 67.95400 ymin,ymax (A): -8.667000 53.21800 zmin,zma (A): -1.247000 61.41900 x,y,z range (A): 64.65900 61.88500 62.66600 scale (grids/A): 2.477613 object centre (A): 35.62450 22.27550 30.08600 number of atom coordinates read : 5195 total number of charged atoms : 5043 net assigned charge : -0.3789458 assigned positive charge : 796.4135 centred at (gu) : 80.07368 86.63198 87.28553 assigned negative charge : -796.7986 centred at (gu) : 79.53598 86.80051 87.08751 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 263753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40831 grid for indexing accessible points = 1.400000 m= 130222 mr = 199993 m= 40328 mr = 106191 m= 7267 mr = 31206 m= 588 mr = 4932 m= 12 mr = 290 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 1.380000 number of dielectric boundary points 99558 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 40297 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) : 1.651742 object centre at (A) : 35.62450 22.27550 30.08600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3860669 -0.3493797 midg,1,midg; midg,igrid,midg 0.1077885 -3.7092227E-02 1,midg,midg; igrid,midg,midg -0.4892036 0.1918600 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.630000 now iterating at: 18:06:47 rms-change max change #iterations 12.18168 340.2578 at 10iterations 7.157621 136.5743 at 20iterations 4.187348 80.71185 at 30iterations 2.438176 51.08734 at 40iterations 1.411770 24.33297 at 50iterations 0.8173426 13.74668 at 60iterations 0.4712036 8.342579 at 70iterations 0.2716197 4.481534 at 80iterations 0.1568298 2.721063 at 90iterations 9.0437576E-02 1.551594 at 100iterations 5.2233208E-02 0.8434401 at 110iterations 3.0319784E-02 0.5340958 at 120iterations 1.7806206E-02 0.2902184 at 130iterations 1.0707489E-02 0.1701174 at 140iterations 6.6987947E-03 0.1124306 at 150iterations 4.4311476E-03 7.5442314E-02 at 160iterations 3.1477003E-03 5.3440213E-02 at 170iterations 2.3862461E-03 3.7719727E-02 at 180iterations finished qdiffx linear iterations at : 18:06:59 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 2.3862461E-03 3.7719727E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 18:07:00 13.646u 0.190s 0:14.11 98.0% 0+0k 0+0io 0pf+0w