Mon Oct 10 14:00:47 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 14:00:47 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 = 4656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5405651 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): 21.39600 78.77600 ymin,ymax (A): 118.9750 184.8320 zmin,zma (A): -1.841000 59.94200 x,y,z range (A): 57.38000 65.85700 61.78300 scale (grids/A): 0.5405651 object centre (A): 50.08600 151.9035 29.05050 number of atom coordinates read : 4656 total number of charged atoms : 4487 net assigned charge : 3.000036 assigned positive charge : 710.0580 centred at (gu) : 90.83024 89.26717 87.36029 assigned negative charge : -707.0617 centred at (gu) : 90.84908 89.18867 87.41220 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8672 nv = 96 ne = 84 npr = 94041 no. pairs analyzed = 94041 no. exposed pairs = 5727 no. arc points = 39420 no. surface atoms = 1917 nbur = 2739 mkacc time = 0.2600000 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= 386 mr = 4636 m= 0 mr = 24 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 4398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4031 ## 550 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11671 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1434120E-09 -1.5369075E-10 midg,1,midg; midg,igrid,midg -6.4363836E-10 6.7073214E-10 1,midg,midg; igrid,midg,midg 2.4731103E-10 -2.3525352E-11 gauss-seidel spectral radius is 0.9824820 estimated iterations to convergence 62 setup time was (sec) 0.8100000 now iterating at: 14:00:48 rms-change max change #iterations 8.9015290E-02 16.74523 at 10iterations 7.0922859E-03 1.093208 at 20iterations 2.0792100E-03 0.3669128 at 30iterations 1.0191092E-03 0.1800499 at 40iterations 5.0906441E-04 8.9393616E-02 at 50iterations finished qdiffx linear iterations at : 14:00:52 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 5.0906441E-04 8.9393616E-02 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 14:00:53 4.288u 0.258s 0:05.24 86.4% 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 14:00:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.621695 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): 21.39600 78.77600 ymin,ymax (A): 118.9750 184.8320 zmin,zma (A): -1.841000 59.94200 x,y,z range (A): 57.38000 65.85700 61.78300 scale (grids/A): 1.621695 object centre (A): 50.08600 151.9035 29.05050 number of atom coordinates read : 4656 total number of charged atoms : 4487 net assigned charge : 3.000036 assigned positive charge : 710.0580 centred at (gu) : 92.48939 87.80034 82.07972 assigned negative charge : -707.0617 centred at (gu) : 92.54697 87.56588 82.23647 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 98456 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30746 mr = 69250 m= 3296 mr = 20866 m= 98 mr = 1626 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 40842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 34235 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) : 0.5405651 object centre at (A) : 50.08600 151.9035 29.05050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7089990E-03 9.4970278E-03 midg,1,midg; midg,igrid,midg 1.2307287E-02 2.8988566E-02 1,midg,midg; igrid,midg,midg -1.6624320E-02 -1.4482570E-02 gauss-seidel spectral radius is 0.9983207 estimated iterations to convergence 194 setup time was (sec) 1.180000 now iterating at: 14:00:54 rms-change max change #iterations 4.307918 178.3381 at 10iterations 1.853014 62.61763 at 20iterations 0.7962499 26.66161 at 30iterations 0.3448002 10.74277 at 40iterations 0.1488551 4.740733 at 50iterations 6.4650767E-02 1.945786 at 60iterations 2.8401760E-02 0.8648434 at 70iterations 1.2853145E-02 0.3664856 at 80iterations 6.3178460E-03 0.2125645 at 90iterations 3.6023476E-03 0.1354446 at 100iterations 2.4168396E-03 8.3171844E-02 at 110iterations 1.7898262E-03 5.9978485E-02 at 120iterations finished qdiffx linear iterations at : 14:01:03 total time elapsed so far: 9.690000 # loops : 120 mean,max change (kT/e) : 1.7898262E-03 5.9978485E-02 energy calculations done at 9.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.870000 DelPhi exited at 14:01:04 9.876u 0.288s 0:10.94 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 14:01:04 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 = 4656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.432543 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): 21.39600 78.77600 ymin,ymax (A): 118.9750 184.8320 zmin,zma (A): -1.841000 59.94200 x,y,z range (A): 57.38000 65.85700 61.78300 scale (grids/A): 2.432543 object centre (A): 50.08600 151.9035 29.05050 number of atom coordinates read : 4656 total number of charged atoms : 4487 net assigned charge : 3.000036 assigned positive charge : 710.0580 centred at (gu) : 93.73383 86.70029 78.11935 assigned negative charge : -707.0617 centred at (gu) : 93.82038 86.34869 78.35474 start vw surface at 0.2100000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 229157 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39420 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107311 mr = 169382 m= 30469 mr = 84772 m= 5300 mr = 22650 m= 404 mr = 3503 m= 9 mr = 185 m= 0 mr = 2 time to grow re-entrant surface = 1.320000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.130000 number of dielectric boundary points 92156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 35849 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) : 1.621695 object centre at (A) : 50.08600 151.9035 29.05050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3599541E-02 0.2196141 midg,1,midg; midg,igrid,midg 0.1817057 0.4955298 1,midg,midg; igrid,midg,midg -0.2832359 -0.1970643 gauss-seidel spectral radius is 0.9992133 estimated iterations to convergence 281 setup time was (sec) 2.470000 now iterating at: 14:01:06 rms-change max change #iterations 11.07702 274.9094 at 10iterations 6.445230 138.7413 at 20iterations 3.717256 76.19322 at 30iterations 2.133559 38.60719 at 40iterations 1.223923 24.04592 at 50iterations 0.6987382 12.07676 at 60iterations 0.3977131 8.203222 at 70iterations 0.2261384 4.061682 at 80iterations 0.1286419 2.380773 at 90iterations 7.3118784E-02 1.233356 at 100iterations 4.1623503E-02 0.7352943 at 110iterations 2.3793055E-02 0.4554482 at 120iterations 1.3716587E-02 0.2543945 at 130iterations 8.0739167E-03 0.1556005 at 140iterations 4.9355803E-03 0.1009636 at 150iterations 3.2287773E-03 7.2727203E-02 at 160iterations 2.2968638E-03 5.0964355E-02 at 170iterations 1.7650106E-03 3.8303375E-02 at 180iterations finished qdiffx linear iterations at : 14:01:21 total time elapsed so far: 16.69000 # loops : 180 mean,max change (kT/e) : 1.7650106E-03 3.8303375E-02 energy calculations done at 16.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.87000 DelPhi exited at 14:01:22 16.874u 0.320s 0:17.88 96.1% 0+0k 0+0io 0pf+0w