Tue Nov 22 14:10:59 PST 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 Tue Nov 22 2011 at 14:11:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 0.6248574 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): -35.04500 10.49100 ymin,ymax (A): 0.9990000 41.55900 zmin,zma (A): -1.461000 55.51200 x,y,z range (A): 45.53600 40.56000 56.97300 scale (grids/A): 0.6248574 object centre (A): -12.27700 21.27900 27.02550 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 287.5540 centred at (gu) : 90.30454 89.44077 90.54868 assigned negative charge : -284.5543 centred at (gu) : 90.23264 89.57251 90.56406 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5164 nv = 96 ne = 84 npr = 40431 no. pairs analyzed = 40431 no. exposed pairs = 2393 no. arc points = 16841 no. surface atoms = 811 nbur = 1147 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 252 mr = 2809 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1674 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6112 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2119150E-09 2.1117339E-09 midg,1,midg; midg,igrid,midg 1.1342774E-08 -4.1735997E-09 1,midg,midg; igrid,midg,midg -1.2180178E-09 7.2126420E-09 gauss-seidel spectral radius is 0.9866777 estimated iterations to convergence 71 setup time was (sec) 0.5000000 now iterating at: 14:11:04 rms-change max change #iterations 0.1109921 18.64627 at 10iterations 1.0236865E-02 1.890015 at 20iterations 9.4836851E-04 0.1488364 at 30iterations 8.8232300E-05 1.5949249E-02 at 40iterations 8.1993039E-06 1.5134811E-03 at 50iterations finished qdiffx linear iterations at : 14:11:12 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 8.1993039E-06 1.5134811E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:11:13 3.390u 0.172s 0:12.14 29.3% 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 Nov 22 2011 at 14:11:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 1.874572 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): -35.04500 10.49100 ymin,ymax (A): 0.9990000 41.55900 zmin,zma (A): -1.461000 55.51200 x,y,z range (A): 45.53600 40.56000 56.97300 scale (grids/A): 1.874572 object centre (A): -12.27700 21.27900 27.02550 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 287.5540 centred at (gu) : 90.91355 88.32249 91.64585 assigned negative charge : -284.5543 centred at (gu) : 90.69827 88.71758 91.69221 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 55362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16841 grid for indexing accessible points = 1.400000 m= 19999 mr = 38152 m= 2745 mr = 14896 m= 153 mr = 1694 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 0.4400000 number of dielectric boundary points 23470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14325 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) : 0.6248574 object centre at (A) : -12.27700 21.27900 27.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1373274E-02 3.5273571E-02 midg,1,midg; midg,igrid,midg 2.5610181E-03 -7.9603558E-03 1,midg,midg; igrid,midg,midg -3.4639121E-03 -5.4118509E-04 gauss-seidel spectral radius is 0.9985133 estimated iterations to convergence 206 setup time was (sec) 0.7300000 now iterating at: 14:11:15 rms-change max change #iterations 3.445512 165.0034 at 10iterations 1.565410 64.55494 at 20iterations 0.7078281 28.18394 at 30iterations 0.3210624 12.03251 at 40iterations 0.1456134 5.104598 at 50iterations 6.6053934E-02 3.034771 at 60iterations 2.9675229E-02 1.058279 at 70iterations 1.3548513E-02 0.4884309 at 80iterations 6.1487001E-03 0.2169623 at 90iterations 2.7700388E-03 0.1036043 at 100iterations 1.2587127E-03 4.9051285E-02 at 110iterations 5.6972355E-04 2.2366047E-02 at 120iterations finished qdiffx linear iterations at : 14:11:32 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 5.6972355E-04 2.2366047E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 14:11:33 7.679u 0.214s 0:18.62 42.3% 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 Nov 22 2011 at 14:11:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 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: 2.811858 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): -35.04500 10.49100 ymin,ymax (A): 0.9990000 41.55900 zmin,zma (A): -1.461000 55.51200 x,y,z range (A): 45.53600 40.56000 56.97300 scale (grids/A): 2.811858 object centre (A): -12.27700 21.27900 27.02550 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 3.000004 assigned positive charge : 287.5540 centred at (gu) : 91.37045 87.48376 92.46870 assigned negative charge : -284.5543 centred at (gu) : 91.04733 88.07641 92.53844 start vw surface at 0.1200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 127930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16841 grid for indexing accessible points = 1.400000 m= 65130 mr = 92242 m= 22877 mr = 53780 m= 4897 mr = 18450 m= 618 mr = 3599 m= 25 mr = 406 m= 0 mr = 4 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 689 time to turn everything in is 1.090000 number of dielectric boundary points 52996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 14608 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) : 1.874572 object centre at (A) : -12.27700 21.27900 27.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5281019E-02 0.2791615 midg,1,midg; midg,igrid,midg -4.3642864E-02 -0.1040738 1,midg,midg; igrid,midg,midg -7.9273656E-02 -5.5525318E-02 gauss-seidel spectral radius is 0.9992071 estimated iterations to convergence 280 setup time was (sec) 1.420000 now iterating at: 14:11:38 rms-change max change #iterations 8.245412 333.8046 at 10iterations 4.732765 122.9607 at 20iterations 2.683884 62.47738 at 30iterations 1.518483 36.35480 at 40iterations 0.8580831 17.89421 at 50iterations 0.4834752 9.824988 at 60iterations 0.2721011 5.940491 at 70iterations 0.1534144 3.276031 at 80iterations 8.6507142E-02 1.771135 at 90iterations 4.8628993E-02 0.9878993 at 100iterations 2.7360968E-02 0.5880394 at 110iterations 1.5353034E-02 0.3314133 at 120iterations 8.6599812E-03 0.1859055 at 130iterations 4.8632906E-03 0.1087034 at 140iterations 2.7273716E-03 5.6299210E-02 at 150iterations 1.5379189E-03 3.2233238E-02 at 160iterations 8.6634565E-04 1.8454552E-02 at 170iterations 4.8619357E-04 1.0055661E-02 at 180iterations finished qdiffx linear iterations at : 14:12:01 total time elapsed so far: 13.28000 # loops : 180 mean,max change (kT/e) : 4.8619357E-04 1.0055661E-02 energy calculations done at 13.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 14:12:02 13.474u 0.216s 0:28.48 48.0% 0+0k 0+0io 0pf+0w