Sun Oct 9 09:35:24 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 09:35:24 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 = 2730 !!! WARNING: GLN 1020 has a net charge of -0.2720 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: 0.5718141 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): -80.78800 -33.18500 ymin,ymax (A): -35.55800 26.70000 zmin,zma (A): -51.76900 8.035000 x,y,z range (A): 47.60300 62.25800 59.80400 scale (grids/A): 0.5718141 object centre (A): -56.98650 -4.429000 -21.86700 number of atom coordinates read : 2730 total number of charged atoms : 2586 net assigned charge : 0.7280161 assigned positive charge : 403.5566 centred at (gu) : 89.55588 89.11814 87.92815 assigned negative charge : -402.8295 centred at (gu) : 89.58382 89.34113 87.97133 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6012 nv = 96 ne = 84 npr = 53118 no. pairs analyzed = 53118 no. exposed pairs = 3828 no. arc points = 27116 no. surface atoms = 1275 nbur = 1455 mkacc time = 9.9999994E-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 = 1.512000 m= 291 mr = 2961 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2713 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7636 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1895787E-09 -3.5325329E-10 midg,1,midg; midg,igrid,midg 4.1391521E-09 -2.7329992E-09 1,midg,midg; igrid,midg,midg 5.4705401E-10 -3.1421277E-10 gauss-seidel spectral radius is 0.9842082 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 09:35:24 rms-change max change #iterations 8.5382514E-02 14.31495 at 10iterations 6.4526843E-03 1.114304 at 20iterations 4.9582269E-04 8.2412720E-02 at 30iterations 4.2485619E-05 7.0610046E-03 at 40iterations 7.1249692E-06 1.7914772E-03 at 50iterations finished qdiffx linear iterations at : 09:35:27 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 7.1249692E-06 1.7914772E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 09:35:28 3.526u 0.186s 0:04.03 91.8% 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 09:35:28 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 = 2730 !!! WARNING: GLN 1020 has a net charge of -0.2720 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: 1.715442 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): -80.78800 -33.18500 ymin,ymax (A): -35.55800 26.70000 zmin,zma (A): -51.76900 8.035000 x,y,z range (A): 47.60300 62.25800 59.80400 scale (grids/A): 1.715442 object centre (A): -56.98650 -4.429000 -21.86700 number of atom coordinates read : 2730 total number of charged atoms : 2586 net assigned charge : 0.7280161 assigned positive charge : 403.5566 centred at (gu) : 88.66683 87.35394 83.78391 assigned negative charge : -402.8295 centred at (gu) : 88.75125 88.02310 83.91379 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27116 grid for indexing accessible points = 1.400000 m= 21188 mr = 42743 m= 2642 mr = 14471 m= 124 mr = 1324 m= 5 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.3400000 number of dielectric boundary points 30891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20050 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) : 0.5718141 object centre at (A) : -56.98650 -4.429000 -21.86700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3351212E-03 2.4162841E-03 midg,1,midg; midg,igrid,midg 8.8506266E-03 -1.4604546E-02 1,midg,midg; igrid,midg,midg 8.0692340E-03 3.1015982E-03 gauss-seidel spectral radius is 0.9983453 estimated iterations to convergence 195 setup time was (sec) 0.5700000 now iterating at: 09:35:29 rms-change max change #iterations 3.508432 203.0540 at 10iterations 1.509343 54.07950 at 20iterations 0.6521562 25.46355 at 30iterations 0.2817380 9.752113 at 40iterations 0.1221200 4.371720 at 50iterations 5.2813668E-02 1.962158 at 60iterations 2.2900991E-02 0.8959198 at 70iterations 9.8759374E-03 0.3410745 at 80iterations 4.3100202E-03 0.1653366 at 90iterations 1.8650832E-03 6.0994148E-02 at 100iterations 8.0905674E-04 2.8403282E-02 at 110iterations 3.5119648E-04 1.2823105E-02 at 120iterations finished qdiffx linear iterations at : 09:35:36 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 3.5119648E-04 1.2823105E-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) 8.230000 DelPhi exited at 09:35:37 8.235u 0.222s 0:08.72 96.9% 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 Sun Oct 9 2011 at 09:35:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: GLN 1020 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.573164 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): -80.78800 -33.18500 ymin,ymax (A): -35.55800 26.70000 zmin,zma (A): -51.76900 8.035000 x,y,z range (A): 47.60300 62.25800 59.80400 scale (grids/A): 2.573164 object centre (A): -56.98650 -4.429000 -21.86700 number of atom coordinates read : 2730 total number of charged atoms : 2586 net assigned charge : 0.7280161 assigned positive charge : 403.5566 centred at (gu) : 87.99996 86.03072 80.67554 assigned negative charge : -402.8295 centred at (gu) : 88.12681 87.03466 80.87066 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 151552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27116 grid for indexing accessible points = 1.400000 m= 70766 mr = 104580 m= 22673 mr = 55238 m= 4289 mr = 17081 m= 482 mr = 2844 m= 9 mr = 233 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 504 time to turn everything in is 0.8300000 number of dielectric boundary points 69795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20679 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) : 1.715442 object centre at (A) : -56.98650 -4.429000 -21.86700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.0875166E-02 -5.4752571E-03 midg,1,midg; midg,igrid,midg 0.2301625 0.1628501 1,midg,midg; igrid,midg,midg 0.1230955 6.6242263E-02 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 1.100000 now iterating at: 09:35:38 rms-change max change #iterations 8.863468 289.6938 at 10iterations 5.090885 125.0540 at 20iterations 2.893872 66.93573 at 30iterations 1.639000 38.43201 at 40iterations 0.9255627 20.63105 at 50iterations 0.5203685 10.98775 at 60iterations 0.2928080 6.110425 at 70iterations 0.1645576 3.697090 at 80iterations 9.1944739E-02 1.852392 at 90iterations 5.1617444E-02 1.090173 at 100iterations 2.8913679E-02 0.5813222 at 110iterations 1.6191041E-02 0.3118501 at 120iterations 9.0981368E-03 0.1780167 at 130iterations 5.1034587E-03 9.9413872E-02 at 140iterations 2.8725881E-03 5.6765556E-02 at 150iterations 1.6296036E-03 3.8187027E-02 at 160iterations 9.3674503E-04 2.4823666E-02 at 170iterations 5.5131636E-04 1.3933182E-02 at 180iterations finished qdiffx linear iterations at : 09:35:50 total time elapsed so far: 13.18000 # loops : 180 mean,max change (kT/e) : 5.5131636E-04 1.3933182E-02 energy calculations done at 13.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 09:35:51 13.318u 0.241s 0:14.05 96.4% 0+0k 0+0io 0pf+0w