Sun Oct 9 15:07:19 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 15:07:19 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 = 5728 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5085859 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): -16.39200 53.60600 ymin,ymax (A): 97.17101 163.4580 zmin,zma (A): -29.97700 32.51800 x,y,z range (A): 69.99800 66.28700 62.49500 scale (grids/A): 0.5085859 object centre (A): 18.60700 130.3145 1.270500 number of atom coordinates read : 5728 total number of charged atoms : 5556 net assigned charge : -6.999959 assigned positive charge : 876.7632 centred at (gu) : 89.89957 88.85565 88.30791 assigned negative charge : -883.7708 centred at (gu) : 89.95185 88.95895 88.25123 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9049 nv = 96 ne = 84 npr = 118863 no. pairs analyzed = 118863 no. exposed pairs = 6510 no. arc points = 45254 no. surface atoms = 2206 nbur = 3522 mkacc time = 0.2100000 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 = 1.680000 m= 318 mr = 5039 m= 0 mr = 8 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3800000 number of dielectric boundary points 4320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4334 ## 643 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 12368 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0614681E-10 4.5903708E-11 midg,1,midg; midg,igrid,midg 2.8421918E-10 -2.9405442E-10 1,midg,midg; igrid,midg,midg 6.2822837E-11 -2.3887306E-10 gauss-seidel spectral radius is 0.9802806 estimated iterations to convergence 59 setup time was (sec) 0.5900000 now iterating at: 15:07:20 rms-change max change #iterations 7.3244251E-02 9.561800 at 10iterations 4.5307670E-03 0.6661987 at 20iterations 5.4530025E-04 7.4122429E-02 at 30iterations 1.3808876E-04 1.9849777E-02 at 40iterations 4.1702802E-05 5.5513382E-03 at 50iterations finished qdiffx linear iterations at : 15:07:23 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 4.1702802E-05 5.5513382E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 15:07:24 3.664u 0.200s 0:04.14 93.2% 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 Sun Oct 9 2011 at 15:07:24 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 = 5728 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.525758 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): -16.39200 53.60600 ymin,ymax (A): 97.17101 163.4580 zmin,zma (A): -29.97700 32.51800 x,y,z range (A): 69.99800 66.28700 62.49500 scale (grids/A): 1.525758 object centre (A): 18.60700 130.3145 1.270500 number of atom coordinates read : 5728 total number of charged atoms : 5556 net assigned charge : -6.999959 assigned positive charge : 876.7632 centred at (gu) : 89.69687 86.56501 84.92216 assigned negative charge : -883.7708 centred at (gu) : 89.85545 86.87638 84.75338 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 104115 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45254 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29885 mr = 74452 m= 2639 mr = 20673 m= 62 mr = 1140 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3538 time to turn everything in is 0.5000000 number of dielectric boundary points 40437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 613 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 41674 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) : 0.5085859 object centre at (A) : 18.60700 130.3145 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1725652E-04 -8.8947167E-04 midg,1,midg; midg,igrid,midg 6.2762694E-03 -2.0831272E-02 1,midg,midg; igrid,midg,midg -2.1773970E-02 -1.4308127E-02 gauss-seidel spectral radius is 0.9981576 estimated iterations to convergence 185 setup time was (sec) 0.7200000 now iterating at: 15:07:25 rms-change max change #iterations 4.228143 145.9131 at 10iterations 1.753529 53.53488 at 20iterations 0.7284530 21.90846 at 30iterations 0.3025946 9.477792 at 40iterations 0.1254424 3.837421 at 50iterations 5.2289572E-02 1.583541 at 60iterations 2.1785408E-02 0.6584804 at 70iterations 9.0187602E-03 0.2511330 at 80iterations 3.7679560E-03 0.1140442 at 90iterations 1.5814598E-03 4.6813011E-02 at 100iterations 6.6639349E-04 1.9355774E-02 at 110iterations 2.8664971E-04 8.4457397E-03 at 120iterations finished qdiffx linear iterations at : 15:07:32 total time elapsed so far: 8.000000 # loops : 120 mean,max change (kT/e) : 2.8664971E-04 8.4457397E-03 energy calculations done at 8.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 15:07:32 8.138u 0.211s 0:08.67 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 Sun Oct 9 2011 at 15:07:32 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 = 5728 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.288637 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): -16.39200 53.60600 ymin,ymax (A): 97.17101 163.4580 zmin,zma (A): -29.97700 32.51800 x,y,z range (A): 69.99800 66.28700 62.49500 scale (grids/A): 2.288637 object centre (A): 18.60700 130.3145 1.270500 number of atom coordinates read : 5728 total number of charged atoms : 5556 net assigned charge : -6.999959 assigned positive charge : 876.7632 centred at (gu) : 89.54468 84.84710 82.38266 assigned negative charge : -883.7708 centred at (gu) : 89.78300 85.31436 82.12996 start vw surface at 0.1400000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 243374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45254 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 108977 mr = 182505 m= 27127 mr = 87115 m= 3786 mr = 20232 m= 189 mr = 2323 m= 2 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 11519 time to turn everything in is 1.210000 number of dielectric boundary points 91219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 44307 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) : 1.525758 object centre at (A) : 18.60700 130.3145 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9012370E-02 -9.0380281E-02 midg,1,midg; midg,igrid,midg 8.3885945E-02 -0.4429222 1,midg,midg; igrid,midg,midg -0.3001975 -0.1678356 gauss-seidel spectral radius is 0.9991814 estimated iterations to convergence 276 setup time was (sec) 1.450000 now iterating at: 15:07:34 rms-change max change #iterations 11.34020 297.1672 at 10iterations 6.507894 145.8352 at 20iterations 3.702649 86.93077 at 30iterations 2.098251 46.08535 at 40iterations 1.185593 24.11818 at 50iterations 0.6677651 13.15323 at 60iterations 0.3762857 6.767409 at 70iterations 0.2116129 3.682147 at 80iterations 0.1185932 2.106079 at 90iterations 6.6570997E-02 1.186538 at 100iterations 3.7291311E-02 0.6976471 at 110iterations 2.0929214E-02 0.3445168 at 120iterations 1.1692757E-02 0.1960087 at 130iterations 6.5651699E-03 0.1062059 at 140iterations 3.6690836E-03 6.7157745E-02 at 150iterations 2.0536112E-03 3.3359528E-02 at 160iterations 1.1550975E-03 1.9791603E-02 at 170iterations 6.4831466E-04 1.1078835E-02 at 180iterations finished qdiffx linear iterations at : 15:07:46 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 6.4831466E-04 1.1078835E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 15:07:46 13.477u 0.234s 0:14.13 96.9% 0+0k 0+0io 0pf+0w