Tue Oct 11 03:48:43 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 Tue Oct 11 2011 at 03:48:43 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3236 !!! WARNING: GLU 287 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6061947 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): -10.41800 36.97700 ymin,ymax (A): -27.42400 21.46800 zmin,zma (A): -13.29600 45.43100 x,y,z range (A): 47.39500 48.89200 58.72700 scale (grids/A): 0.6061947 object centre (A): 13.27950 -2.978000 16.06750 number of atom coordinates read : 3236 total number of charged atoms : 2815 net assigned charge : -4.859979 assigned positive charge : 450.5862 centred at (gu) : 89.69530 91.18664 92.28915 assigned negative charge : -455.4470 centred at (gu) : 89.50610 91.17043 92.17132 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7113 nv = 96 ne = 84 npr = 61291 no. pairs analyzed = 61291 no. exposed pairs = 3506 no. arc points = 24203 no. surface atoms = 1176 nbur = 2060 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 4056 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3600000 number of dielectric boundary points 3364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2430 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2748859E-09 5.7896057E-09 midg,1,midg; midg,igrid,midg -2.6815588E-09 -2.3350475E-09 1,midg,midg; igrid,midg,midg -1.3485828E-08 6.4056462E-09 gauss-seidel spectral radius is 0.9859369 estimated iterations to convergence 69 setup time was (sec) 0.5900000 now iterating at: 03:48:44 rms-change max change #iterations 0.1229711 17.16382 at 10iterations 1.0768733E-02 1.507750 at 20iterations 9.7637606E-04 0.1284065 at 30iterations 1.0868824E-04 1.4658928E-02 at 40iterations 2.1407464E-05 3.0002594E-03 at 50iterations finished qdiffx linear iterations at : 03:48:47 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.1407464E-05 3.0002594E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:48:47 3.423u 0.141s 0:03.96 89.8% 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 Tue Oct 11 2011 at 03:48:47 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3236 !!! WARNING: GLU 287 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.818584 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): -10.41800 36.97700 ymin,ymax (A): -27.42400 21.46800 zmin,zma (A): -13.29600 45.43100 x,y,z range (A): 47.39500 48.89200 58.72700 scale (grids/A): 1.818584 object centre (A): 13.27950 -2.978000 16.06750 number of atom coordinates read : 3236 total number of charged atoms : 2815 net assigned charge : -4.859979 assigned positive charge : 450.5862 centred at (gu) : 89.08544 93.55914 96.86672 assigned negative charge : -455.4470 centred at (gu) : 88.51794 93.51059 96.51335 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24203 grid for indexing accessible points = 1.400000 m= 27456 mr = 55131 m= 3759 mr = 20437 m= 166 mr = 2251 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3517 time to turn everything in is 0.5800000 number of dielectric boundary points 31071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 21980 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) : 0.6061947 object centre at (A) : 13.27950 -2.978000 16.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3789943E-02 -3.2821685E-04 midg,1,midg; midg,igrid,midg -8.6529283E-03 -2.6810402E-02 1,midg,midg; igrid,midg,midg -1.5779940E-02 2.6619885E-02 gauss-seidel spectral radius is 0.9985347 estimated iterations to convergence 207 setup time was (sec) 0.8600000 now iterating at: 03:48:48 rms-change max change #iterations 4.250322 176.1035 at 10iterations 1.933833 68.79494 at 20iterations 0.8839411 30.73334 at 30iterations 0.4038564 13.99672 at 40iterations 0.1844244 6.963928 at 50iterations 8.3968490E-02 2.688487 at 60iterations 3.8523488E-02 1.254513 at 70iterations 1.7606366E-02 0.5338304 at 80iterations 8.0100866E-03 0.2517109 at 90iterations 3.6846318E-03 0.1189040 at 100iterations 1.7014029E-03 5.8166027E-02 at 110iterations 7.8772253E-04 2.4604797E-02 at 120iterations finished qdiffx linear iterations at : 03:48:55 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 7.8772253E-04 2.4604797E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 03:48:56 7.984u 0.214s 0:08.48 96.5% 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 Tue Oct 11 2011 at 03:48:56 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3236 !!! WARNING: GLU 287 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.727876 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): -10.41800 36.97700 ymin,ymax (A): -27.42400 21.46800 zmin,zma (A): -13.29600 45.43100 x,y,z range (A): 47.39500 48.89200 58.72700 scale (grids/A): 2.727876 object centre (A): 13.27950 -2.978000 16.06750 number of atom coordinates read : 3236 total number of charged atoms : 2815 net assigned charge : -4.859979 assigned positive charge : 450.5862 centred at (gu) : 88.62780 95.33852 100.3000 assigned negative charge : -455.4470 centred at (gu) : 87.77687 95.26578 99.77010 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 179439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24203 grid for indexing accessible points = 1.400000 m= 90891 mr = 133249 m= 30948 mr = 75075 m= 6427 mr = 24964 m= 701 mr = 4756 m= 28 mr = 424 m= 0 mr = 7 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 11619 time to turn everything in is 1.440000 number of dielectric boundary points 69959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 22520 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) : 1.818584 object centre at (A) : 13.27950 -2.978000 16.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.046737 0.2546417 midg,1,midg; midg,igrid,midg -0.1118667 -0.3932547 1,midg,midg; igrid,midg,midg -0.1657556 0.2766865 gauss-seidel spectral radius is 0.9992302 estimated iterations to convergence 285 setup time was (sec) 1.750000 now iterating at: 03:48:58 rms-change max change #iterations 10.08982 371.3732 at 10iterations 5.834098 150.2057 at 20iterations 3.358083 77.57535 at 30iterations 1.927957 39.79446 at 40iterations 1.101417 20.78141 at 50iterations 0.6306638 11.57730 at 60iterations 0.3595493 6.886864 at 70iterations 0.2052869 3.772255 at 80iterations 0.1169281 2.189476 at 90iterations 6.6662684E-02 1.232494 at 100iterations 3.8078964E-02 0.7270908 at 110iterations 2.1669839E-02 0.3799744 at 120iterations 1.2361686E-02 0.2274742 at 130iterations 7.0674298E-03 0.1476402 at 140iterations 4.0325401E-03 7.0369720E-02 at 150iterations 2.3223287E-03 3.9501190E-02 at 160iterations 1.3419499E-03 2.3795128E-02 at 170iterations 7.8749756E-04 1.5361786E-02 at 180iterations finished qdiffx linear iterations at : 03:49:08 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 7.8749756E-04 1.5361786E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 03:49:09 12.498u 0.213s 0:13.19 96.2% 0+0k 0+0io 0pf+0w