Sun Oct 9 07:21:44 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 Sun Oct 9 2011 at 07:21:44 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5452513 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): -4.720000 42.09700 ymin,ymax (A): 35.82800 87.22701 zmin,zma (A): -3.599000 61.69200 x,y,z range (A): 46.81700 51.39900 65.29100 scale (grids/A): 0.5452513 object centre (A): 18.68850 61.52750 29.04650 number of atom coordinates read : 2478 total number of charged atoms : 2333 net assigned charge : -10.49998 assigned positive charge : 372.3359 centred at (gu) : 90.64849 89.10506 89.47211 assigned negative charge : -382.8364 centred at (gu) : 90.81208 88.74266 89.38494 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4857 nv = 96 ne = 84 npr = 49366 no. pairs analyzed = 49366 no. exposed pairs = 3458 no. arc points = 24944 no. surface atoms = 1162 nbur = 1316 mkacc time = 9.0000004E-02 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= 186 mr = 2268 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 2773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2459 ## 297 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6250 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2403417E-09 -1.0926124E-10 midg,1,midg; midg,igrid,midg -3.3900847E-09 1.0532386E-09 1,midg,midg; igrid,midg,midg 2.4277638E-10 -1.7942908E-09 gauss-seidel spectral radius is 0.9826274 estimated iterations to convergence 62 setup time was (sec) 0.3700000 now iterating at: 07:21:45 rms-change max change #iterations 6.5012656E-02 12.93779 at 10iterations 4.1375407E-03 0.8709164 at 20iterations 2.7798998E-04 5.8766901E-02 at 30iterations 1.8705367E-05 3.6983490E-03 at 40iterations 1.4374948E-06 2.8324127E-04 at 50iterations finished qdiffx linear iterations at : 07:21:47 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.4374948E-06 2.8324127E-04 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 07:21:48 3.352u 0.168s 0:03.80 92.3% 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 07:21:48 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.635754 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): -4.720000 42.09700 ymin,ymax (A): 35.82800 87.22701 zmin,zma (A): -3.599000 61.69200 x,y,z range (A): 46.81700 51.39900 65.29100 scale (grids/A): 1.635754 object centre (A): 18.68850 61.52750 29.04650 number of atom coordinates read : 2478 total number of charged atoms : 2333 net assigned charge : -10.49998 assigned positive charge : 372.3359 centred at (gu) : 91.94488 87.31470 88.41579 assigned negative charge : -382.8364 centred at (gu) : 92.43591 86.22793 88.15446 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 53054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24944 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15576 mr = 33392 m= 1433 mr = 10254 m= 33 mr = 590 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 82 time to turn everything in is 0.2700000 number of dielectric boundary points 25860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 17919 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) : 0.5452513 object centre at (A) : 18.68850 61.52750 29.04650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4410790E-02 4.1396688E-03 midg,1,midg; midg,igrid,midg -2.3358092E-02 7.1653859E-03 1,midg,midg; igrid,midg,midg -2.3435035E-03 -1.5887802E-02 gauss-seidel spectral radius is 0.9981402 estimated iterations to convergence 184 setup time was (sec) 0.4800000 now iterating at: 07:21:49 rms-change max change #iterations 3.025063 160.5739 at 10iterations 1.242449 58.77698 at 20iterations 0.5103197 20.31050 at 30iterations 0.2095183 8.372143 at 40iterations 8.6067669E-02 3.490477 at 50iterations 3.5479754E-02 1.455528 at 60iterations 1.4608661E-02 0.5435184 at 70iterations 6.0034785E-03 0.2431602 at 80iterations 2.4740333E-03 0.1094244 at 90iterations 1.0183739E-03 3.6552429E-02 at 100iterations 4.1987121E-04 1.7297745E-02 at 110iterations 1.7283089E-04 7.7667236E-03 at 120iterations finished qdiffx linear iterations at : 07:21:56 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.7283089E-04 7.7667236E-03 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 07:21:56 7.554u 0.188s 0:08.01 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 Sun Oct 9 2011 at 07:21:56 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.453631 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): -4.720000 42.09700 ymin,ymax (A): 35.82800 87.22701 zmin,zma (A): -3.599000 61.69200 x,y,z range (A): 46.81700 51.39900 65.29100 scale (grids/A): 2.453631 object centre (A): 18.68850 61.52750 29.04650 number of atom coordinates read : 2478 total number of charged atoms : 2333 net assigned charge : -10.49998 assigned positive charge : 372.3359 centred at (gu) : 92.91715 85.97184 87.62358 assigned negative charge : -382.8364 centred at (gu) : 93.65388 84.34177 87.23158 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 122966 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24944 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 54334 mr = 82192 m= 14458 mr = 41830 m= 2022 mr = 10331 m= 117 mr = 1135 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 310 time to turn everything in is 0.6300000 number of dielectric boundary points 58369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18649 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) : 1.635754 object centre at (A) : 18.68850 61.52750 29.04650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7763506 3.4367748E-02 midg,1,midg; midg,igrid,midg -0.3196830 9.9403270E-02 1,midg,midg; igrid,midg,midg -2.9541096E-02 -0.2049633 gauss-seidel spectral radius is 0.9991159 estimated iterations to convergence 266 setup time was (sec) 0.8600000 now iterating at: 07:21:57 rms-change max change #iterations 7.891463 365.3185 at 10iterations 4.386489 141.1051 at 20iterations 2.433418 66.29348 at 30iterations 1.342857 37.03291 at 40iterations 0.7396419 18.18458 at 50iterations 0.4061780 9.873130 at 60iterations 0.2227799 5.255852 at 70iterations 0.1218755 2.771994 at 80iterations 6.6666186E-02 1.513355 at 90iterations 3.6409952E-02 0.8078570 at 100iterations 1.9934475E-02 0.4677582 at 110iterations 1.0874204E-02 0.2423477 at 120iterations 5.9263748E-03 0.1412249 at 130iterations 3.2283915E-03 7.8208923E-02 at 140iterations 1.7604897E-03 4.3430328E-02 at 150iterations 9.5885713E-04 2.3170471E-02 at 160iterations 5.2249583E-04 1.1209488E-02 at 170iterations 2.8523654E-04 6.7958832E-03 at 180iterations finished qdiffx linear iterations at : 07:22:08 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 2.8523654E-04 6.7958832E-03 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 07:22:08 11.929u 0.197s 0:12.42 97.5% 0+0k 0+0io 0pf+0w