Tue Oct 11 07:52:12 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 Tue Oct 11 2011 at 07:52:12 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 0.6373417 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): -9.058001 39.75000 ymin,ymax (A): -14.93800 40.91900 zmin,zma (A): 5.456000 52.57900 x,y,z range (A): 48.80800 55.85700 47.12300 scale (grids/A): 0.6373417 object centre (A): 15.34600 12.99050 29.01750 number of atom coordinates read : 2358 total number of charged atoms : 2216 net assigned charge : 3.931008 assigned positive charge : 352.7374 centred at (gu) : 89.50907 88.82371 90.58035 assigned negative charge : -348.8069 centred at (gu) : 89.43323 88.84733 90.74699 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6518 nv = 96 ne = 84 npr = 47030 no. pairs analyzed = 47030 no. exposed pairs = 2863 no. arc points = 20402 no. surface atoms = 973 nbur = 1385 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3631 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.3600000 number of dielectric boundary points 3166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1987 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7710 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8838934E-08 -1.2640623E-08 midg,1,midg; midg,igrid,midg 9.9096358E-09 2.4733529E-09 1,midg,midg; igrid,midg,midg -2.2799245E-09 1.1475489E-08 gauss-seidel spectral radius is 0.9872256 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 07:52:13 rms-change max change #iterations 0.1376110 19.80753 at 10iterations 1.3834567E-02 2.062136 at 20iterations 1.4599555E-03 0.2152710 at 30iterations 1.7398610E-04 2.9182434E-02 at 40iterations 2.5364974E-05 4.0931702E-03 at 50iterations finished qdiffx linear iterations at : 07:52:16 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 2.5364974E-05 4.0931702E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 07:52:17 4.233u 0.212s 0:04.72 94.0% 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 Tue Oct 11 2011 at 07:52:17 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 1.912025 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): -9.058001 39.75000 ymin,ymax (A): -14.93800 40.91900 zmin,zma (A): 5.456000 52.57900 x,y,z range (A): 48.80800 55.85700 47.12300 scale (grids/A): 1.912025 object centre (A): 15.34600 12.99050 29.01750 number of atom coordinates read : 2358 total number of charged atoms : 2216 net assigned charge : 3.931008 assigned positive charge : 352.7374 centred at (gu) : 88.52680 86.47094 91.74074 assigned negative charge : -348.8069 centred at (gu) : 88.29958 86.54184 92.24097 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20402 grid for indexing accessible points = 1.400000 m= 26140 mr = 49063 m= 3927 mr = 19524 m= 243 mr = 2484 m= 3 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 795 time to turn everything in is 0.6500000 number of dielectric boundary points 29187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 17392 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) : 0.6373417 object centre at (A) : 15.34600 12.99050 29.01750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7221525E-02 -2.0810725E-02 midg,1,midg; midg,igrid,midg 2.6082583E-02 1.8785331E-02 1,midg,midg; igrid,midg,midg -5.4830057E-03 5.0230026E-03 gauss-seidel spectral radius is 0.9986227 estimated iterations to convergence 214 setup time was (sec) 1.020000 now iterating at: 07:52:18 rms-change max change #iterations 4.028897 187.4509 at 10iterations 1.878118 67.75871 at 20iterations 0.8839511 29.77579 at 30iterations 0.4118203 14.45557 at 40iterations 0.1929063 6.262464 at 50iterations 9.0505674E-02 3.062582 at 60iterations 4.2203803E-02 1.438820 at 70iterations 1.9771453E-02 0.6463432 at 80iterations 9.2654312E-03 0.2932816 at 90iterations 4.3650069E-03 0.1408157 at 100iterations 2.0420582E-03 6.3690186E-02 at 110iterations 9.6287148E-04 3.3492088E-02 at 120iterations finished qdiffx linear iterations at : 07:52:26 total time elapsed so far: 9.120000 # loops : 120 mean,max change (kT/e) : 9.6287148E-04 3.3492088E-02 energy calculations done at 9.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 07:52:27 9.345u 0.243s 0:09.90 96.7% 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 Tue Oct 11 2011 at 07:52:27 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 2.868038 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): -9.058001 39.75000 ymin,ymax (A): -14.93800 40.91900 zmin,zma (A): 5.456000 52.57900 x,y,z range (A): 48.80800 55.85700 47.12300 scale (grids/A): 2.868038 object centre (A): 15.34600 12.99050 29.01750 number of atom coordinates read : 2358 total number of charged atoms : 2216 net assigned charge : 3.931008 assigned positive charge : 352.7374 centred at (gu) : 87.79013 84.70643 92.61119 assigned negative charge : -348.8069 centred at (gu) : 87.44930 84.81281 93.36143 start vw surface at 0.1800000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 161919 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20402 grid for indexing accessible points = 1.400000 m= 84351 mr = 118509 m= 30370 mr = 69833 m= 6997 mr = 24558 m= 1063 mr = 5348 m= 64 mr = 760 m= 0 mr = 27 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2907 time to turn everything in is 1.670000 number of dielectric boundary points 65729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 17720 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) : 1.912025 object centre at (A) : 15.34600 12.99050 29.01750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4362504 -0.3115966 midg,1,midg; midg,igrid,midg 0.2215290 0.1932059 1,midg,midg; igrid,midg,midg -3.5853516E-02 -6.0162414E-03 gauss-seidel spectral radius is 0.9992483 estimated iterations to convergence 288 setup time was (sec) 2.050000 now iterating at: 07:52:29 rms-change max change #iterations 9.444466 284.8201 at 10iterations 5.495633 135.7942 at 20iterations 3.185432 72.94529 at 30iterations 1.839566 38.66135 at 40iterations 1.059080 20.93743 at 50iterations 0.6085699 10.77036 at 60iterations 0.3498620 7.204234 at 70iterations 0.2002730 4.049092 at 80iterations 0.1148846 2.026306 at 90iterations 6.5725617E-02 1.256180 at 100iterations 3.7689518E-02 0.6661758 at 110iterations 2.1696072E-02 0.4498789 at 120iterations 1.2384780E-02 0.2496672 at 130iterations 7.1050404E-03 0.1321774 at 140iterations 4.0991264E-03 8.0336213E-02 at 150iterations 2.3702581E-03 5.1269531E-02 at 160iterations 1.3769359E-03 2.6123047E-02 at 170iterations 8.0998818E-04 1.5539169E-02 at 180iterations finished qdiffx linear iterations at : 07:52:42 total time elapsed so far: 14.89000 # loops : 180 mean,max change (kT/e) : 8.0998818E-04 1.5539169E-02 energy calculations done at 14.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.13000 DelPhi exited at 07:52:43 15.135u 0.238s 0:15.93 96.4% 0+0k 0+0io 0pf+0w