Sat Oct 15 12:27:49 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 15 2011 at 12:27:49 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6875772 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): -21.37900 25.39700 ymin,ymax (A): -26.26800 25.50800 zmin,zma (A): -13.95800 36.39700 x,y,z range (A): 46.77600 51.77600 50.35500 scale (grids/A): 0.6875772 object centre (A): 2.009001 -0.3799992 11.21950 number of atom coordinates read : 2019 total number of charged atoms : 1879 net assigned charge : 1.5392900E-05 assigned positive charge : 304.9929 centred at (gu) : 89.62041 89.90000 89.71574 assigned negative charge : -304.9930 centred at (gu) : 89.76436 89.88137 89.77150 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6499 nv = 96 ne = 84 npr = 41766 no. pairs analyzed = 41766 no. exposed pairs = 2478 no. arc points = 17712 no. surface atoms = 836 nbur = 1183 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 3653 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.1600000 number of dielectric boundary points 3204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1598 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7285 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7807512E-08 -1.6403153E-08 midg,1,midg; midg,igrid,midg -6.0406480E-09 5.3934119E-09 1,midg,midg; igrid,midg,midg 4.6792501E-08 -4.1618254E-08 gauss-seidel spectral radius is 0.9889801 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 12:27:49 rms-change max change #iterations 0.1739611 24.20460 at 10iterations 2.0492157E-02 3.308395 at 20iterations 2.3974779E-03 0.3512697 at 30iterations 2.7549820E-04 3.9388657E-02 at 40iterations 3.1430409E-05 4.2867661E-03 at 50iterations finished qdiffx linear iterations at : 12:27:52 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.1430409E-05 4.2867661E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 12:27:53 3.363u 0.169s 0:03.89 90.4% 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 Sat Oct 15 2011 at 12:27:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.062732 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): -21.37900 25.39700 ymin,ymax (A): -26.26800 25.50800 zmin,zma (A): -13.95800 36.39700 x,y,z range (A): 46.77600 51.77600 50.35500 scale (grids/A): 2.062732 object centre (A): 2.009001 -0.3799992 11.21950 number of atom coordinates read : 2019 total number of charged atoms : 1879 net assigned charge : 1.5392900E-05 assigned positive charge : 304.9929 centred at (gu) : 88.86142 89.70016 89.14715 assigned negative charge : -304.9930 centred at (gu) : 89.29295 89.64413 89.31445 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17712 grid for indexing accessible points = 1.400000 m= 27229 mr = 47155 m= 5404 mr = 20876 m= 425 mr = 3718 m= 7 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1561 time to turn everything in is 0.3500000 number of dielectric boundary points 29471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14872 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) : 0.6875772 object centre at (A) : 2.009001 -0.3799992 11.21950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7861349E-03 -5.3140908E-02 midg,1,midg; midg,igrid,midg 1.4401155E-02 -2.9430036E-02 1,midg,midg; igrid,midg,midg 4.4130109E-02 -1.0298790E-02 gauss-seidel spectral radius is 0.9987727 estimated iterations to convergence 226 setup time was (sec) 0.5600000 now iterating at: 12:27:54 rms-change max change #iterations 4.439075 301.8815 at 10iterations 2.138820 81.24590 at 20iterations 1.043486 37.84584 at 30iterations 0.5075377 16.66530 at 40iterations 0.2466968 7.314707 at 50iterations 0.1202381 3.626302 at 60iterations 5.8493603E-02 1.865971 at 70iterations 2.8473299E-02 0.9184752 at 80iterations 1.3936293E-02 0.4271855 at 90iterations 6.7789285E-03 0.2142258 at 100iterations 3.3026985E-03 0.1065521 at 110iterations 1.6048353E-03 5.2211761E-02 at 120iterations finished qdiffx linear iterations at : 12:28:01 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.6048353E-03 5.2211761E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 12:28:01 7.762u 0.214s 0:08.29 96.1% 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 15 2011 at 12:28:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.094098 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): -21.37900 25.39700 ymin,ymax (A): -26.26800 25.50800 zmin,zma (A): -13.95800 36.39700 x,y,z range (A): 46.77600 51.77600 50.35500 scale (grids/A): 3.094098 object centre (A): 2.009001 -0.3799992 11.21950 number of atom coordinates read : 2019 total number of charged atoms : 1879 net assigned charge : 1.5392900E-05 assigned positive charge : 304.9929 centred at (gu) : 88.29219 89.55021 88.72076 assigned negative charge : -304.9930 centred at (gu) : 88.93941 89.46617 88.97167 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 157138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17712 grid for indexing accessible points = 1.400000 m= 83629 mr = 113051 m= 35407 mr = 69744 m= 10474 mr = 29628 m= 1834 mr = 8304 m= 160 mr = 1338 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 5135 time to turn everything in is 1.050000 number of dielectric boundary points 66495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 15028 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) : 2.062732 object centre at (A) : 2.009001 -0.3799992 11.21950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4001093E-02 -0.7365543 midg,1,midg; midg,igrid,midg 0.2337060 -0.5285586 1,midg,midg; igrid,midg,midg 0.4212736 -0.1314042 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 1.280000 now iterating at: 12:28:03 rms-change max change #iterations 9.952791 414.1722 at 10iterations 5.780269 129.8590 at 20iterations 3.368633 81.31540 at 30iterations 1.955230 38.19137 at 40iterations 1.133737 23.72966 at 50iterations 0.6609194 11.67980 at 60iterations 0.3821796 7.516956 at 70iterations 0.2212094 3.899960 at 80iterations 0.1283343 2.419964 at 90iterations 7.4514739E-02 1.426580 at 100iterations 4.3169256E-02 0.8069525 at 110iterations 2.4984935E-02 0.4585495 at 120iterations 1.4471162E-02 0.2761040 at 130iterations 8.3812568E-03 0.1613221 at 140iterations 4.8568365E-03 0.1049728 at 150iterations 2.8139285E-03 4.9032211E-02 at 160iterations 1.6339815E-03 2.9933929E-02 at 170iterations 9.4437232E-04 1.9165993E-02 at 180iterations finished qdiffx linear iterations at : 12:28:14 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 9.4437232E-04 1.9165993E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.80000 DelPhi exited at 12:28:15 12.806u 0.215s 0:13.37 97.3% 0+0k 0+0io 0pf+0w