Tue Oct 11 06:45:00 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 06:45:00 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7021835 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): 3.437000 45.96300 ymin,ymax (A): 0.5340000 41.26300 zmin,zma (A): -3.584000 47.11500 x,y,z range (A): 42.52600 40.72900 50.69900 scale (grids/A): 0.7021835 object centre (A): 24.70000 20.89850 21.76550 number of atom coordinates read : 2019 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.9771 centred at (gu) : 90.38641 90.33756 90.63244 assigned negative charge : -307.0461 centred at (gu) : 90.58065 90.29656 90.65800 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6853 nv = 96 ne = 84 npr = 39654 no. pairs analyzed = 39654 no. exposed pairs = 2451 no. arc points = 17026 no. surface atoms = 831 nbur = 1188 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 3925 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3302 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1633 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7686 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5911450E-08 4.6113417E-08 midg,1,midg; midg,igrid,midg 3.2207918E-08 7.4387280E-08 1,midg,midg; igrid,midg,midg 1.2459799E-07 -3.6554777E-08 gauss-seidel spectral radius is 0.9894246 estimated iterations to convergence 79 setup time was (sec) 0.5300000 now iterating at: 06:45:01 rms-change max change #iterations 0.1902038 28.51080 at 10iterations 2.3799472E-02 3.594347 at 20iterations 3.0226745E-03 0.4086075 at 30iterations 4.4121401E-04 6.1868906E-02 at 40iterations 9.2541624E-05 1.3612747E-02 at 50iterations finished qdiffx linear iterations at : 06:45:04 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 9.2541624E-05 1.3612747E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 06:45:05 4.351u 0.310s 0:04.99 93.3% 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 Tue Oct 11 2011 at 06:45:05 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.106550 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): 3.437000 45.96300 ymin,ymax (A): 0.5340000 41.26300 zmin,zma (A): -3.584000 47.11500 x,y,z range (A): 42.52600 40.72900 50.69900 scale (grids/A): 2.106550 object centre (A): 24.70000 20.89850 21.76550 number of atom coordinates read : 2019 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.9771 centred at (gu) : 91.15945 91.01273 91.89735 assigned negative charge : -307.0461 centred at (gu) : 91.74185 90.88996 91.97426 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17026 grid for indexing accessible points = 1.400000 m= 28717 mr = 51609 m= 5607 mr = 21790 m= 531 mr = 3753 m= 8 mr = 265 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15334 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) : 0.7021835 object centre at (A) : 24.70000 20.89850 21.76550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1468941E-02 6.4035237E-02 midg,1,midg; midg,igrid,midg 7.3403772E-04 3.1426940E-02 1,midg,midg; igrid,midg,midg 4.1095961E-02 1.1015561E-02 gauss-seidel spectral radius is 0.9988105 estimated iterations to convergence 230 setup time was (sec) 0.9600000 now iterating at: 06:45:06 rms-change max change #iterations 4.526126 217.4820 at 10iterations 2.224980 70.76836 at 20iterations 1.098204 33.76867 at 30iterations 0.5438015 17.06739 at 40iterations 0.2688709 8.489445 at 50iterations 0.1325979 4.174896 at 60iterations 6.5593690E-02 1.960561 at 70iterations 3.2368619E-02 0.9691045 at 80iterations 1.6023621E-02 0.4973335 at 90iterations 7.9851197E-03 0.2537594 at 100iterations 3.9930246E-03 0.1386986 at 110iterations 2.0226685E-03 6.1108589E-02 at 120iterations finished qdiffx linear iterations at : 06:45:15 total time elapsed so far: 9.980000 # loops : 120 mean,max change (kT/e) : 2.0226685E-03 6.1108589E-02 energy calculations done at 9.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.16000 DelPhi exited at 06:45:16 10.159u 0.343s 0:10.90 96.2% 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 Tue Oct 11 2011 at 06:45:16 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2019 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.159826 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): 3.437000 45.96300 ymin,ymax (A): 0.5340000 41.26300 zmin,zma (A): -3.584000 47.11500 x,y,z range (A): 42.52600 40.72900 50.69900 scale (grids/A): 3.159826 object centre (A): 24.70000 20.89850 21.76550 number of atom coordinates read : 2019 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.9771 centred at (gu) : 91.73910 91.51905 92.84597 assigned negative charge : -307.0461 centred at (gu) : 92.61275 91.33484 92.96131 start vw surface at 0.1300000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 167439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17026 grid for indexing accessible points = 1.400000 m= 90563 mr = 124400 m= 36099 mr = 75332 m= 10544 mr = 29699 m= 2059 mr = 8078 m= 201 mr = 1507 m= 7 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 67768 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15448 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) : 2.106550 object centre at (A) : 24.70000 20.89850 21.76550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3473781 0.6683756 midg,1,midg; midg,igrid,midg -3.3945810E-02 0.2434787 1,midg,midg; igrid,midg,midg 0.3292988 0.3003453 gauss-seidel spectral radius is 0.9992881 estimated iterations to convergence 296 setup time was (sec) 2.200000 now iterating at: 06:45:18 rms-change max change #iterations 10.12063 437.7843 at 10iterations 5.958130 144.3353 at 20iterations 3.511232 68.77127 at 30iterations 2.065372 44.21511 at 40iterations 1.209500 22.29832 at 50iterations 0.7099181 14.02661 at 60iterations 0.4146640 8.322070 at 70iterations 0.2421688 4.285499 at 80iterations 0.1415797 2.532242 at 90iterations 8.2898721E-02 1.740104 at 100iterations 4.8306402E-02 0.8752484 at 110iterations 2.8373295E-02 0.5030155 at 120iterations 1.6669266E-02 0.2980857 at 130iterations 9.8720472E-03 0.2110064 at 140iterations 5.9401393E-03 0.1081161 at 150iterations 3.6403860E-03 6.6539764E-02 at 160iterations 2.3270133E-03 4.6108246E-02 at 170iterations 1.5560237E-03 2.7706146E-02 at 180iterations finished qdiffx linear iterations at : 06:45:33 total time elapsed so far: 16.65000 # loops : 180 mean,max change (kT/e) : 1.5560237E-03 2.7706146E-02 energy calculations done at 16.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.84000 DelPhi exited at 06:45:34 16.839u 0.353s 0:17.71 97.0% 0+0k 0+0io 0pf+0w