Sun Oct 9 15:07:26 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 15:07:26 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 = 5528 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: 0.5152849 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): -16.64500 52.44300 ymin,ymax (A): 98.36800 167.1420 zmin,zma (A): -34.98600 31.79000 x,y,z range (A): 69.08800 68.77402 66.77600 scale (grids/A): 0.5152849 object centre (A): 17.89900 132.7550 -1.598000 number of atom coordinates read : 5528 total number of charged atoms : 5354 net assigned charge : -3.999962 assigned positive charge : 848.4916 centred at (gu) : 89.68207 88.86961 89.07317 assigned negative charge : -852.4987 centred at (gu) : 89.67283 88.93342 89.05975 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9053 nv = 96 ne = 84 npr = 112939 no. pairs analyzed = 112939 no. exposed pairs = 6494 no. arc points = 45524 no. surface atoms = 2188 nbur = 3340 mkacc time = 0.2000000 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 = 4918 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3600000 number of dielectric boundary points 4449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4383 ## 635 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 12243 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5631131E-10 -1.7498883E-11 midg,1,midg; midg,igrid,midg 2.2626150E-10 -2.3422789E-10 1,midg,midg; igrid,midg,midg -1.1614001E-10 -3.4562554E-11 gauss-seidel spectral radius is 0.9807808 estimated iterations to convergence 60 setup time was (sec) 0.5800000 now iterating at: 15:07:27 rms-change max change #iterations 7.8145593E-02 11.69650 at 10iterations 6.4606969E-03 0.9474335 at 20iterations 1.5187848E-03 0.2680435 at 30iterations 4.7802267E-04 8.2363129E-02 at 40iterations 1.5219559E-04 2.6004791E-02 at 50iterations finished qdiffx linear iterations at : 15:07:30 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 1.5219559E-04 2.6004791E-02 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 15:07:31 3.802u 0.199s 0:04.31 92.5% 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 15:07:31 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 = 5528 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.545855 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): -16.64500 52.44300 ymin,ymax (A): 98.36800 167.1420 zmin,zma (A): -34.98600 31.79000 x,y,z range (A): 69.08800 68.77402 66.77600 scale (grids/A): 1.545855 object centre (A): 17.89900 132.7550 -1.598000 number of atom coordinates read : 5528 total number of charged atoms : 5354 net assigned charge : -3.999962 assigned positive charge : 848.4916 centred at (gu) : 89.04446 86.60700 87.21782 assigned negative charge : -852.4987 centred at (gu) : 89.01842 86.79987 87.17898 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103436 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45524 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30704 mr = 72963 m= 2689 mr = 21111 m= 54 mr = 1228 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2376 time to turn everything in is 0.5000000 number of dielectric boundary points 41579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 558 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 40311 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) : 0.5152849 object centre at (A) : 17.89900 132.7550 -1.598000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5656484E-02 -1.0509348E-02 midg,1,midg; midg,igrid,midg 2.5051899E-02 -1.7453324E-02 1,midg,midg; igrid,midg,midg -3.3713181E-02 -1.1866317E-02 gauss-seidel spectral radius is 0.9982003 estimated iterations to convergence 187 setup time was (sec) 0.7400000 now iterating at: 15:07:32 rms-change max change #iterations 4.278062 161.0118 at 10iterations 1.790311 56.75202 at 20iterations 0.7535247 22.98472 at 30iterations 0.3160597 9.492742 at 40iterations 0.1327980 4.105790 at 50iterations 5.5988576E-02 1.637146 at 60iterations 2.3697352E-02 0.6829071 at 70iterations 1.0244888E-02 0.3193922 at 80iterations 4.5527848E-03 0.1467838 at 90iterations 2.1482303E-03 7.6133728E-02 at 100iterations 1.1129666E-03 3.9703369E-02 at 110iterations 6.3214102E-04 2.3235321E-02 at 120iterations finished qdiffx linear iterations at : 15:07:39 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 6.3214102E-04 2.3235321E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 15:07:40 8.434u 0.236s 0:08.96 96.6% 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 Sun Oct 9 2011 at 15:07:40 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 = 5528 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.318782 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): -16.64500 52.44300 ymin,ymax (A): 98.36800 167.1420 zmin,zma (A): -34.98600 31.79000 x,y,z range (A): 69.08800 68.77402 66.77600 scale (grids/A): 2.318782 object centre (A): 17.89900 132.7550 -1.598000 number of atom coordinates read : 5528 total number of charged atoms : 5354 net assigned charge : -3.999962 assigned positive charge : 848.4916 centred at (gu) : 88.56628 84.90997 85.82619 assigned negative charge : -852.4987 centred at (gu) : 88.52761 85.19969 85.76854 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 241095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45524 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 109533 mr = 178964 m= 29061 mr = 87014 m= 3987 mr = 21587 m= 214 mr = 2464 m= 7 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 7732 time to turn everything in is 1.230000 number of dielectric boundary points 93810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 42740 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) : 1.545855 object centre at (A) : 17.89900 132.7550 -1.598000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3196577 -0.2351288 midg,1,midg; midg,igrid,midg 0.5804422 -0.2750605 1,midg,midg; igrid,midg,midg -0.4042059 -0.3215382 gauss-seidel spectral radius is 0.9991945 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 15:07:41 rms-change max change #iterations 11.39340 267.5427 at 10iterations 6.558973 138.9744 at 20iterations 3.748628 93.04660 at 30iterations 2.126651 55.92049 at 40iterations 1.209789 27.95896 at 50iterations 0.6843308 15.39710 at 60iterations 0.3859978 7.969643 at 70iterations 0.2180395 3.940598 at 80iterations 0.1227594 2.196850 at 90iterations 6.9168769E-02 1.250839 at 100iterations 3.8861740E-02 0.7736359 at 110iterations 2.1899320E-02 0.3801537 at 120iterations 1.2317661E-02 0.2014923 at 130iterations 6.9537181E-03 0.1202908 at 140iterations 3.9282334E-03 7.3211670E-02 at 150iterations 2.2333139E-03 3.8003385E-02 at 160iterations 1.2799588E-03 2.1695137E-02 at 170iterations 7.4727047E-04 1.5188217E-02 at 180iterations finished qdiffx linear iterations at : 15:07:54 total time elapsed so far: 13.88000 # loops : 180 mean,max change (kT/e) : 7.4727047E-04 1.5188217E-02 energy calculations done at 13.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 15:07:54 14.021u 0.237s 0:14.56 97.8% 0+0k 0+0io 0pf+0w