Sun Oct 9 11:20:49 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 Sun Oct 9 2011 at 11:20:50 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: CME 445 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5432212 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): 9.527000 67.05400 ymin,ymax (A): -34.53200 31.00300 zmin,zma (A): -7.356000 45.23800 x,y,z range (A): 57.52700 65.53500 52.59400 scale (grids/A): 0.5432212 object centre (A): 38.29050 -1.764501 18.94100 number of atom coordinates read : 2760 total number of charged atoms : 2613 net assigned charge : 1.117013 assigned positive charge : 397.8214 centred at (gu) : 87.78548 91.18677 89.86575 assigned negative charge : -396.7058 centred at (gu) : 87.86345 91.24717 90.04146 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5454 nv = 96 ne = 84 npr = 54429 no. pairs analyzed = 54429 no. exposed pairs = 3869 no. arc points = 27293 no. surface atoms = 1292 nbur = 1468 mkacc time = 9.0000004E-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 = 1.596000 m= 221 mr = 2582 m= 0 mr = 4 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2695 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7085 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0007171E-09 -8.6752494E-10 midg,1,midg; midg,igrid,midg 2.7801850E-10 -3.6289280E-10 1,midg,midg; igrid,midg,midg 8.1786644E-10 -2.0737212E-10 gauss-seidel spectral radius is 0.9825264 estimated iterations to convergence 62 setup time was (sec) 0.3800000 now iterating at: 11:20:50 rms-change max change #iterations 6.5689564E-02 12.07574 at 10iterations 4.2907107E-03 0.7090225 at 20iterations 2.9340171E-04 5.5618763E-02 at 30iterations 2.3956150E-05 4.3373108E-03 at 40iterations 3.2072244E-06 5.3977966E-04 at 50iterations finished qdiffx linear iterations at : 11:20:53 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 3.2072244E-06 5.3977966E-04 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:20:54 3.741u 0.188s 0:04.22 92.8% 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 11:20:54 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: CME 445 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of 0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.629663 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): 9.527000 67.05400 ymin,ymax (A): -34.53200 31.00300 zmin,zma (A): -7.356000 45.23800 x,y,z range (A): 57.52700 65.53500 52.59400 scale (grids/A): 1.629663 object centre (A): 38.29050 -1.764501 18.94100 number of atom coordinates read : 2760 total number of charged atoms : 2613 net assigned charge : 1.117013 assigned positive charge : 397.8214 centred at (gu) : 83.35577 93.55991 89.59658 assigned negative charge : -396.7058 centred at (gu) : 83.59026 93.74139 90.12423 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17627 mr = 39573 m= 1817 mr = 11398 m= 55 mr = 826 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.3000000 number of dielectric boundary points 28621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 280 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 20066 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) : 0.5432212 object centre at (A) : 38.29050 -1.764501 18.94100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2281934E-02 -1.5985738E-02 midg,1,midg; midg,igrid,midg 6.2143435E-03 -1.2321983E-02 1,midg,midg; igrid,midg,midg 8.4341150E-03 -8.4223533E-03 gauss-seidel spectral radius is 0.9981731 estimated iterations to convergence 186 setup time was (sec) 0.5200000 now iterating at: 11:20:54 rms-change max change #iterations 3.097059 142.7450 at 10iterations 1.283407 49.07669 at 20iterations 0.5319538 23.34843 at 30iterations 0.2213045 8.897064 at 40iterations 9.1487207E-02 3.589863 at 50iterations 3.8130969E-02 1.460602 at 60iterations 1.5820540E-02 0.6780796 at 70iterations 6.5788627E-03 0.2467995 at 80iterations 2.7318192E-03 0.1043510 at 90iterations 1.1360177E-03 4.2407990E-02 at 100iterations 4.7537175E-04 1.8941879E-02 at 110iterations 1.9863590E-04 7.3819160E-03 at 120iterations finished qdiffx linear iterations at : 11:21:02 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.9863590E-04 7.3819160E-03 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 11:21:02 7.719u 0.201s 0:08.26 95.7% 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 Sun Oct 9 2011 at 11:21:02 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2760 !!! WARNING: CME 445 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.1350 !!! WARNING: CME 3 has a net charge of 0.1000 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: 2.444495 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): 9.527000 67.05400 ymin,ymax (A): -34.53200 31.00300 zmin,zma (A): -7.356000 45.23800 x,y,z range (A): 57.52700 65.53500 52.59400 scale (grids/A): 2.444495 object centre (A): 38.29050 -1.764501 18.94100 number of atom coordinates read : 2760 total number of charged atoms : 2613 net assigned charge : 1.117013 assigned positive charge : 397.8214 centred at (gu) : 80.03344 95.33944 89.39460 assigned negative charge : -396.7058 centred at (gu) : 80.38546 95.61219 90.18638 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 141424 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27293 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61261 mr = 97460 m= 17077 mr = 46613 m= 2844 mr = 12292 m= 199 mr = 1747 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 990 time to turn everything in is 0.7400000 number of dielectric boundary points 64609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 20877 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) : 1.629663 object centre at (A) : 38.29050 -1.764501 18.94100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1784337 -0.2195500 midg,1,midg; midg,igrid,midg 8.8674180E-02 -0.2809426 1,midg,midg; igrid,midg,midg 0.1293017 -0.1437741 gauss-seidel spectral radius is 0.9991348 estimated iterations to convergence 269 setup time was (sec) 0.9800000 now iterating at: 11:21:03 rms-change max change #iterations 8.135542 284.9788 at 10iterations 4.594732 109.7071 at 20iterations 2.581881 62.91875 at 30iterations 1.437953 32.49430 at 40iterations 0.7994845 17.85053 at 50iterations 0.4424068 9.763599 at 60iterations 0.2440432 5.391798 at 70iterations 0.1348405 2.992561 at 80iterations 7.4131250E-02 1.670938 at 90iterations 4.0764224E-02 0.8768048 at 100iterations 2.2404194E-02 0.4973755 at 110iterations 1.2322105E-02 0.2479119 at 120iterations 6.7543597E-03 0.1535854 at 130iterations 3.7144369E-03 8.2655907E-02 at 140iterations 2.0329340E-03 4.3712616E-02 at 150iterations 1.1182697E-03 2.4394989E-02 at 160iterations 6.1317038E-04 1.2985229E-02 at 170iterations 3.3753202E-04 7.3585510E-03 at 180iterations finished qdiffx linear iterations at : 11:21:14 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 3.3753202E-04 7.3585510E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 11:21:15 12.293u 0.201s 0:12.90 96.8% 0+0k 0+0io 0pf+0w