Sat Oct 8 19:30:43 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 19:30:43 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 935 has a net charge of 1.4000 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: 0.6313512 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): -10.31200 38.76300 ymin,ymax (A): -22.08100 24.88700 zmin,zma (A): -12.30600 44.08100 x,y,z range (A): 49.07500 46.96800 56.38700 scale (grids/A): 0.6313512 object centre (A): 14.22550 1.403000 15.88750 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.6441 centred at (gu) : 88.44140 89.21827 89.84691 assigned negative charge : -388.7386 centred at (gu) : 88.32652 89.26611 89.75332 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6651 nv = 96 ne = 84 npr = 55368 no. pairs analyzed = 55368 no. exposed pairs = 2943 no. arc points = 20858 no. surface atoms = 989 nbur = 1604 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3731 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.2000000 number of dielectric boundary points 3187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8213 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2407544E-09 1.2647837E-08 midg,1,midg; midg,igrid,midg 1.0590301E-08 1.7780953E-10 1,midg,midg; igrid,midg,midg -8.7422158E-09 1.0711336E-08 gauss-seidel spectral radius is 0.9869965 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 19:30:44 rms-change max change #iterations 0.1400188 20.16232 at 10iterations 1.3300514E-02 1.889219 at 20iterations 1.2909111E-03 0.2047939 at 30iterations 1.2404329E-04 1.8455505E-02 at 40iterations 1.1999986E-05 1.8310547E-03 at 50iterations finished qdiffx linear iterations at : 19:30:47 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.1999986E-05 1.8310547E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 19:30:47 3.404u 0.176s 0:03.84 92.9% 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 Sat Oct 8 2011 at 19:30:47 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 935 has a net charge of 1.4000 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: 1.894054 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): -10.31200 38.76300 ymin,ymax (A): -22.08100 24.88700 zmin,zma (A): -12.30600 44.08100 x,y,z range (A): 49.07500 46.96800 56.38700 scale (grids/A): 1.894054 object centre (A): 14.22550 1.403000 15.88750 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.6441 centred at (gu) : 85.32352 87.65465 89.54029 assigned negative charge : -388.7386 centred at (gu) : 84.97930 87.79817 89.25983 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20858 grid for indexing accessible points = 1.400000 m= 24948 mr = 51183 m= 3566 mr = 18456 m= 173 mr = 2203 m= 0 mr = 69 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4520 time to turn everything in is 0.3500000 number of dielectric boundary points 29359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19284 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) : 0.6313512 object centre at (A) : 14.22550 1.403000 15.88750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8296957E-02 2.3585789E-02 midg,1,midg; midg,igrid,midg 1.7931722E-02 2.0677175E-03 1,midg,midg; igrid,midg,midg -5.6651030E-03 3.9872948E-02 gauss-seidel spectral radius is 0.9986117 estimated iterations to convergence 213 setup time was (sec) 0.5700000 now iterating at: 19:30:48 rms-change max change #iterations 4.193491 176.3181 at 10iterations 1.945283 63.88996 at 20iterations 0.9099610 28.60200 at 30iterations 0.4223115 14.54474 at 40iterations 0.1970309 6.768993 at 50iterations 9.1723636E-02 3.225582 at 60iterations 4.2820450E-02 1.397842 at 70iterations 1.9891249E-02 0.6158447 at 80iterations 9.2551038E-03 0.2880955 at 90iterations 4.3065003E-03 0.1294436 at 100iterations 2.0047412E-03 6.1523438E-02 at 110iterations 9.3526015E-04 2.7370453E-02 at 120iterations finished qdiffx linear iterations at : 19:30:55 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 9.3526015E-04 2.7370453E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 19:30:55 7.688u 0.205s 0:08.17 96.4% 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 Sat Oct 8 2011 at 19:30:55 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 935 has a net charge of 1.4000 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: 2.841080 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): -10.31200 38.76300 ymin,ymax (A): -22.08100 24.88700 zmin,zma (A): -12.30600 44.08100 x,y,z range (A): 49.07500 46.96800 56.38700 scale (grids/A): 2.841080 object centre (A): 14.22550 1.403000 15.88750 number of atom coordinates read : 2593 total number of charged atoms : 2450 net assigned charge : 3.906009 assigned positive charge : 392.6441 centred at (gu) : 82.98519 86.48178 89.31044 assigned negative charge : -388.7386 centred at (gu) : 82.46884 86.69724 88.88982 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20858 grid for indexing accessible points = 1.400000 m= 83083 mr = 123759 m= 27715 mr = 68497 m= 6215 mr = 22220 m= 742 mr = 4630 m= 43 mr = 525 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 15262 time to turn everything in is 0.8900000 number of dielectric boundary points 66292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19598 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) : 1.894054 object centre at (A) : 14.22550 1.403000 15.88750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1279799 0.3188246 midg,1,midg; midg,igrid,midg 0.1901880 1.8315438E-02 1,midg,midg; igrid,midg,midg -3.1037539E-02 0.5194162 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.130000 now iterating at: 19:30:57 rms-change max change #iterations 9.710924 342.2070 at 10iterations 5.590670 126.4222 at 20iterations 3.200822 69.71488 at 30iterations 1.831814 37.41906 at 40iterations 1.047102 20.20135 at 50iterations 0.5969910 11.72129 at 60iterations 0.3420995 6.508684 at 70iterations 0.1957335 3.533072 at 80iterations 0.1115582 2.277241 at 90iterations 6.3810997E-02 1.193523 at 100iterations 3.6437254E-02 0.6478043 at 110iterations 2.0775486E-02 0.3758230 at 120iterations 1.1873076E-02 0.2218380 at 130iterations 6.7693125E-03 0.1221027 at 140iterations 3.8653065E-03 6.7828178E-02 at 150iterations 2.2050254E-03 4.0042877E-02 at 160iterations 1.2608115E-03 2.3902893E-02 at 170iterations 7.1962312E-04 1.2289047E-02 at 180iterations finished qdiffx linear iterations at : 19:31:08 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 7.1962312E-04 1.2289047E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.35000 DelPhi exited at 19:31:08 12.355u 0.195s 0:12.81 97.8% 0+0k 0+0io 0pf+0w