Sat Oct 8 19:52:58 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 Sat Oct 8 2011 at 19:52:58 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 477 has a net charge of 1.4000 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: 0.6186678 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): -31.89400 17.35400 ymin,ymax (A): -24.27300 22.99300 zmin,zma (A): -12.50300 45.04000 x,y,z range (A): 49.24800 47.26600 57.54300 scale (grids/A): 0.6186678 object centre (A): -7.270000 -0.6399994 16.26850 number of atom coordinates read : 2558 total number of charged atoms : 2470 net assigned charge : 4.000009 assigned positive charge : 393.4340 centred at (gu) : 88.56731 89.42818 89.81043 assigned negative charge : -389.4345 centred at (gu) : 88.46452 89.46601 89.69616 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6462 nv = 96 ne = 84 npr = 52019 no. pairs analyzed = 52019 no. exposed pairs = 3025 no. arc points = 21853 no. surface atoms = 1020 nbur = 1538 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3600 m= 0 mr = 27 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.1900000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2148 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8079 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4001962E-09 9.9911626E-09 midg,1,midg; midg,igrid,midg 6.3594561E-09 6.9331041E-10 1,midg,midg; igrid,midg,midg -4.8604014E-09 7.0869395E-09 gauss-seidel spectral radius is 0.9864650 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 19:52:59 rms-change max change #iterations 0.1246085 18.79769 at 10iterations 1.1556927E-02 1.548199 at 20iterations 1.0778562E-03 0.1604929 at 30iterations 1.1307912E-04 2.1598816E-02 at 40iterations 1.3500674E-05 2.6168823E-03 at 50iterations finished qdiffx linear iterations at : 19:53:03 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.3500674E-05 2.6168823E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 19:53:04 3.644u 0.473s 0:05.84 70.3% 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 Sat Oct 8 2011 at 19:53:04 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 477 has a net charge of 1.4000 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: 1.856003 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): -31.89400 17.35400 ymin,ymax (A): -24.27300 22.99300 zmin,zma (A): -12.50300 45.04000 x,y,z range (A): 49.24800 47.26600 57.54300 scale (grids/A): 1.856003 object centre (A): -7.270000 -0.6399994 16.26850 number of atom coordinates read : 2558 total number of charged atoms : 2470 net assigned charge : 4.000009 assigned positive charge : 393.4340 centred at (gu) : 85.70156 88.28413 89.43079 assigned negative charge : -389.4345 centred at (gu) : 85.39314 88.39778 89.08842 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21853 grid for indexing accessible points = 1.400000 m= 23910 mr = 48695 m= 3402 mr = 17507 m= 151 mr = 2052 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 4571 time to turn everything in is 0.3300000 number of dielectric boundary points 29304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19383 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) : 0.6186678 object centre at (A) : -7.270000 -0.6399994 16.26850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6423412E-02 2.8452752E-02 midg,1,midg; midg,igrid,midg 1.2492123E-02 3.2534015E-03 1,midg,midg; igrid,midg,midg -4.6156091E-03 3.5999060E-02 gauss-seidel spectral radius is 0.9985594 estimated iterations to convergence 209 setup time was (sec) 0.5900000 now iterating at: 19:53:05 rms-change max change #iterations 4.020001 175.9878 at 10iterations 1.848355 59.68734 at 20iterations 0.8434027 31.15919 at 30iterations 0.3879973 12.72860 at 40iterations 0.1784659 6.577663 at 50iterations 8.1731118E-02 3.090082 at 60iterations 3.7680279E-02 1.340149 at 70iterations 1.7270245E-02 0.5528946 at 80iterations 7.9224212E-03 0.2614594 at 90iterations 3.6396079E-03 0.1239624 at 100iterations 1.6657617E-03 5.7601929E-02 at 110iterations 7.6917594E-04 2.6489258E-02 at 120iterations finished qdiffx linear iterations at : 19:53:16 total time elapsed so far: 8.370000 # loops : 120 mean,max change (kT/e) : 7.6917594E-04 2.6489258E-02 energy calculations done at 8.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 19:53:17 8.525u 0.783s 0:12.88 72.2% 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 Sat Oct 8 2011 at 19:53:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2558 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 477 has a net charge of 1.4000 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: 2.784005 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): -31.89400 17.35400 ymin,ymax (A): -24.27300 22.99300 zmin,zma (A): -12.50300 45.04000 x,y,z range (A): 49.24800 47.26600 57.54300 scale (grids/A): 2.784005 object centre (A): -7.270000 -0.6399994 16.26850 number of atom coordinates read : 2558 total number of charged atoms : 2470 net assigned charge : 4.000009 assigned positive charge : 393.4340 centred at (gu) : 83.55233 87.42607 89.14615 assigned negative charge : -389.4345 centred at (gu) : 83.08973 87.59658 88.63245 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 162399 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21853 grid for indexing accessible points = 1.400000 m= 79830 mr = 118158 m= 26706 mr = 65378 m= 5918 mr = 21324 m= 665 mr = 4330 m= 20 mr = 413 m= 0 mr = 3 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 15738 time to turn everything in is 0.8800000 number of dielectric boundary points 65932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 19758 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) : 1.856003 object centre at (A) : -7.270000 -0.6399994 16.26850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5402662E-02 0.3324761 midg,1,midg; midg,igrid,midg 0.1621867 1.5279451E-02 1,midg,midg; igrid,midg,midg -3.8744733E-02 0.4740106 gauss-seidel spectral radius is 0.9992341 estimated iterations to convergence 285 setup time was (sec) 1.140000 now iterating at: 19:53:19 rms-change max change #iterations 9.487590 319.5966 at 10iterations 5.454609 109.7861 at 20iterations 3.120518 68.52166 at 30iterations 1.779919 39.02964 at 40iterations 1.013890 21.50524 at 50iterations 0.5790883 11.73075 at 60iterations 0.3291197 6.257244 at 70iterations 0.1877600 3.708870 at 80iterations 0.1067537 2.157221 at 90iterations 6.0778514E-02 1.225820 at 100iterations 3.4691282E-02 0.6710055 at 110iterations 1.9806821E-02 0.3642044 at 120iterations 1.1260618E-02 0.2156858 at 130iterations 6.4317682E-03 0.1594563 at 140iterations 3.6797114E-03 7.4073792E-02 at 150iterations 2.1167169E-03 4.0555954E-02 at 160iterations 1.2290238E-03 2.7694702E-02 at 170iterations 7.2150573E-04 1.7839432E-02 at 180iterations finished qdiffx linear iterations at : 19:53:37 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 7.2150573E-04 1.7839432E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 19:53:37 13.276u 1.169s 0:20.58 70.1% 0+0k 0+0io 0pf+0w