Sun Oct 9 22:31:13 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 22:31:13 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIZ 21 has a net charge of 0.2000 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: SEP 140 has a net charge of -0.4750 !!! WARNING: ZN1 1035 has a net charge of 1.4000 !!! WARNING: ZN1 1036 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5774440 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): -28.43000 29.28200 ymin,ymax (A): 41.10000 102.7510 zmin,zma (A): 52.20500 109.7260 x,y,z range (A): 57.71200 61.65100 57.52100 scale (grids/A): 0.5774440 object centre (A): 0.4259996 71.92550 80.96550 number of atom coordinates read : 3020 total number of charged atoms : 2905 net assigned charge : 8.425009 assigned positive charge : 466.4059 centred at (gu) : 89.64242 88.85848 90.49206 assigned negative charge : -457.9821 centred at (gu) : 89.64809 88.73782 90.46929 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6734 nv = 96 ne = 84 npr = 56463 no. pairs analyzed = 56463 no. exposed pairs = 4239 no. arc points = 31492 no. surface atoms = 1409 nbur = 1611 mkacc time = 0.1200000 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 = 1.484000 m= 301 mr = 3131 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8619 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1087558E-09 2.4471767E-09 midg,1,midg; midg,igrid,midg -1.1290040E-09 3.2082255E-09 1,midg,midg; igrid,midg,midg 1.9860447E-09 1.4699881E-09 gauss-seidel spectral radius is 0.9845423 estimated iterations to convergence 66 setup time was (sec) 0.5400000 now iterating at: 22:31:14 rms-change max change #iterations 9.7146720E-02 16.61487 at 10iterations 7.3881457E-03 1.260136 at 20iterations 5.6514330E-04 8.2481384E-02 at 30iterations 4.4074113E-05 6.5231323E-03 at 40iterations 3.3570848E-06 6.3323975E-04 at 50iterations finished qdiffx linear iterations at : 22:31:16 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 3.3570848E-06 6.3323975E-04 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 22:31:17 3.304u 0.226s 0:03.83 91.9% 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 22:31:17 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIZ 21 has a net charge of 0.2000 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: SEP 140 has a net charge of -0.4750 !!! WARNING: ZN1 1035 has a net charge of 1.4000 !!! WARNING: ZN1 1036 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.732332 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): -28.43000 29.28200 ymin,ymax (A): 41.10000 102.7510 zmin,zma (A): 52.20500 109.7260 x,y,z range (A): 57.71200 61.65100 57.52100 scale (grids/A): 1.732332 object centre (A): 0.4259996 71.92550 80.96550 number of atom coordinates read : 3020 total number of charged atoms : 2905 net assigned charge : 8.425009 assigned positive charge : 466.4059 centred at (gu) : 88.92632 86.57468 91.47565 assigned negative charge : -457.9821 centred at (gu) : 88.94387 86.21314 91.40758 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73328 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31492 grid for indexing accessible points = 1.400000 m= 22780 mr = 46177 m= 2629 mr = 15039 m= 106 mr = 1297 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 239 time to turn everything in is 0.5200000 number of dielectric boundary points 36317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 22543 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) : 0.5774440 object centre at (A) : 0.4259996 71.92550 80.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3838872E-03 2.4475422E-02 midg,1,midg; midg,igrid,midg -4.3327515E-03 1.2735624E-02 1,midg,midg; igrid,midg,midg 1.5982132E-02 1.6810996E-02 gauss-seidel spectral radius is 0.9984279 estimated iterations to convergence 200 setup time was (sec) 0.7900000 now iterating at: 22:31:18 rms-change max change #iterations 3.848003 178.9359 at 10iterations 1.683398 60.62151 at 20iterations 0.7428427 27.76176 at 30iterations 0.3277358 11.16093 at 40iterations 0.1441806 5.238939 at 50iterations 6.3843064E-02 2.490650 at 60iterations 2.8152728E-02 1.055286 at 70iterations 1.2449397E-02 0.4487305 at 80iterations 5.5055800E-03 0.1831512 at 90iterations 2.4412854E-03 7.8600883E-02 at 100iterations 1.0786562E-03 3.5598755E-02 at 110iterations 4.7705366E-04 1.5345097E-02 at 120iterations finished qdiffx linear iterations at : 22:31:24 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 4.7705366E-04 1.5345097E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 22:31:25 7.415u 0.249s 0:07.98 95.8% 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 22:31:25 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 !!! WARNING: HIZ 21 has a net charge of 0.2000 !!! WARNING: GLM 40 has a net charge of -0.6000 !!! WARNING: SEP 140 has a net charge of -0.4750 !!! WARNING: ZN1 1035 has a net charge of 1.4000 !!! WARNING: ZN1 1036 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.598498 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): -28.43000 29.28200 ymin,ymax (A): 41.10000 102.7510 zmin,zma (A): 52.20500 109.7260 x,y,z range (A): 57.71200 61.65100 57.52100 scale (grids/A): 2.598498 object centre (A): 0.4259996 71.92550 80.96550 number of atom coordinates read : 3020 total number of charged atoms : 2905 net assigned charge : 8.425009 assigned positive charge : 466.4059 centred at (gu) : 88.38907 84.86181 92.21299 assigned negative charge : -457.9821 centred at (gu) : 88.41573 84.31956 92.11127 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 169735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31492 grid for indexing accessible points = 1.400000 m= 76803 mr = 113619 m= 23063 mr = 58956 m= 4161 mr = 16811 m= 438 mr = 2670 m= 6 mr = 227 m= 0 mr = 1 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 875 time to turn everything in is 1.250000 number of dielectric boundary points 81922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 23224 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) : 1.732332 object centre at (A) : 0.4259996 71.92550 80.96550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2238997 0.1052504 midg,1,midg; midg,igrid,midg -0.1926348 0.2707322 1,midg,midg; igrid,midg,midg 0.3247429 0.1247528 gauss-seidel spectral radius is 0.9992281 estimated iterations to convergence 284 setup time was (sec) 1.570000 now iterating at: 22:31:27 rms-change max change #iterations 9.747375 345.3867 at 10iterations 5.711980 148.5771 at 20iterations 3.328086 83.07146 at 30iterations 1.919493 52.93378 at 40iterations 1.107969 24.78565 at 50iterations 0.6359204 13.62846 at 60iterations 0.3647389 8.401790 at 70iterations 0.2090824 4.829544 at 80iterations 0.1194638 2.321269 at 90iterations 6.8025537E-02 1.336510 at 100iterations 3.8803667E-02 0.8067913 at 110iterations 2.2143112E-02 0.4792261 at 120iterations 1.2598455E-02 0.2941294 at 130iterations 7.1816421E-03 0.1438251 at 140iterations 4.0818127E-03 8.6383820E-02 at 150iterations 2.3205809E-03 4.7832489E-02 at 160iterations 1.3193833E-03 2.3525238E-02 at 170iterations 7.4973184E-04 1.5436172E-02 at 180iterations finished qdiffx linear iterations at : 22:31:37 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 7.4973184E-04 1.5436172E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 22:31:37 11.795u 0.261s 0:12.36 97.4% 0+0k 0+0io 0pf+0w