Mon Oct 10 09:15:13 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 Mon Oct 10 2011 at 09:15:13 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 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: 0.6068561 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 0.6068561 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1963 total number of charged atoms : 1811 net assigned charge : 5.000011 assigned positive charge : 288.5490 centred at (gu) : 89.88146 90.21497 90.23222 assigned negative charge : -283.5493 centred at (gu) : 89.88759 90.28770 90.35355 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4859 nv = 96 ne = 84 npr = 40802 no. pairs analyzed = 40802 no. exposed pairs = 2444 no. arc points = 17418 no. surface atoms = 843 nbur = 1120 mkacc time = 7.0000008E-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 = 1.456000 m= 212 mr = 2597 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1791 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2941039E-09 -1.4388233E-09 midg,1,midg; midg,igrid,midg 4.8292659E-09 2.8536568E-10 1,midg,midg; igrid,midg,midg 2.9694081E-09 2.4272928E-09 gauss-seidel spectral radius is 0.9858899 estimated iterations to convergence 69 setup time was (sec) 0.3400000 now iterating at: 09:15:14 rms-change max change #iterations 0.1023822 22.75425 at 10iterations 8.9336382E-03 1.492531 at 20iterations 7.6999463E-04 0.1380157 at 30iterations 6.5258006E-05 1.1779785E-02 at 40iterations 5.7791171E-06 9.5939636E-04 at 50iterations finished qdiffx linear iterations at : 09:15:17 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.7791171E-06 9.5939636E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 09:15:17 3.314u 0.169s 0:03.83 90.6% 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 Mon Oct 10 2011 at 09:15:17 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 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: 1.820568 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 1.820568 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1963 total number of charged atoms : 1811 net assigned charge : 5.000011 assigned positive charge : 288.5490 centred at (gu) : 89.64432 90.64500 90.69668 assigned negative charge : -283.5493 centred at (gu) : 89.66287 90.86337 91.06097 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 52616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17418 grid for indexing accessible points = 1.400000 m= 18362 mr = 35687 m= 2379 mr = 13633 m= 85 mr = 1335 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 22772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 14161 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) : 0.6068561 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6202016E-03 -2.3765753E-04 midg,1,midg; midg,igrid,midg 6.3011157E-03 2.3871029E-03 1,midg,midg; igrid,midg,midg 4.3973833E-02 3.3183251E-02 gauss-seidel spectral radius is 0.9984319 estimated iterations to convergence 200 setup time was (sec) 0.4800000 now iterating at: 09:15:18 rms-change max change #iterations 3.309551 183.2519 at 10iterations 1.458558 54.45158 at 20iterations 0.6483039 27.38063 at 30iterations 0.2866715 11.88111 at 40iterations 0.1273164 4.767002 at 50iterations 5.6176744E-02 2.434436 at 60iterations 2.5075428E-02 0.8797264 at 70iterations 1.1084151E-02 0.4702873 at 80iterations 4.9038287E-03 0.1901336 at 90iterations 2.1690892E-03 8.9092255E-02 at 100iterations 9.6330856E-04 4.3960571E-02 at 110iterations 4.2868650E-04 1.6539574E-02 at 120iterations finished qdiffx linear iterations at : 09:15:25 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 4.2868650E-04 1.6539574E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 09:15:25 7.490u 0.188s 0:08.07 95.0% 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 Mon Oct 10 2011 at 09:15:25 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1963 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: 2.730852 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 2.730852 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1963 total number of charged atoms : 1811 net assigned charge : 5.000011 assigned positive charge : 288.5490 centred at (gu) : 89.46654 90.96734 91.04503 assigned negative charge : -283.5493 centred at (gu) : 89.49442 91.29504 91.59150 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 121483 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17418 grid for indexing accessible points = 1.400000 m= 60271 mr = 86500 m= 20336 mr = 49367 m= 3934 mr = 16421 m= 332 mr = 2740 m= 7 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 51140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14488 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) : 1.820568 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7334890E-02 3.4137789E-02 midg,1,midg; midg,igrid,midg 4.7439724E-02 5.3997301E-02 1,midg,midg; igrid,midg,midg 0.6136476 0.3585184 gauss-seidel spectral radius is 0.9991856 estimated iterations to convergence 277 setup time was (sec) 0.8900000 now iterating at: 09:15:26 rms-change max change #iterations 7.866890 317.1616 at 10iterations 4.451798 119.2360 at 20iterations 2.508357 61.17838 at 30iterations 1.402273 36.18761 at 40iterations 0.7865751 18.22382 at 50iterations 0.4398517 9.734907 at 60iterations 0.2451689 5.362854 at 70iterations 0.1364269 3.021914 at 80iterations 7.6513246E-02 1.752513 at 90iterations 4.2552780E-02 0.9346809 at 100iterations 2.3718225E-02 0.5398064 at 110iterations 1.3274458E-02 0.2855372 at 120iterations 7.3836623E-03 0.1637423 at 130iterations 4.1255327E-03 8.5762024E-02 at 140iterations 2.3000252E-03 4.6508789E-02 at 150iterations 1.2829319E-03 2.6916504E-02 at 160iterations 7.1472052E-04 1.4882088E-02 at 170iterations 3.9895004E-04 1.0042667E-02 at 180iterations finished qdiffx linear iterations at : 09:15:37 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 3.9895004E-04 1.0042667E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 09:15:37 11.707u 0.193s 0:12.24 97.1% 0+0k 0+0io 0pf+0w