Sat Oct 8 19:16:57 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 19:16:57 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! 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: ZN5 556 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6200255 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): -32.22900 17.63400 ymin,ymax (A): -24.88500 21.89200 zmin,zma (A): -12.66800 44.74900 x,y,z range (A): 49.86300 46.77700 57.41700 scale (grids/A): 0.6200255 object centre (A): -7.297500 -1.496500 16.04050 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 88.64141 89.24510 89.92607 assigned negative charge : -390.0956 centred at (gu) : 88.53728 89.27599 89.81371 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6720 nv = 96 ne = 84 npr = 53545 no. pairs analyzed = 53545 no. exposed pairs = 3057 no. arc points = 22087 no. surface atoms = 1019 nbur = 1586 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3815 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 173 time to turn everything in is 0.3000000 number of dielectric boundary points 3193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2201 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9361985E-09 1.0940346E-08 midg,1,midg; midg,igrid,midg 6.8066015E-09 1.4242243E-09 1,midg,midg; igrid,midg,midg -4.5789599E-09 7.8648350E-09 gauss-seidel spectral radius is 0.9865288 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 19:16:58 rms-change max change #iterations 0.1293647 21.88166 at 10iterations 1.1880555E-02 1.793117 at 20iterations 1.1001716E-03 0.1499443 at 30iterations 1.0057957E-04 1.3771057E-02 at 40iterations 9.4536963E-06 1.2798309E-03 at 50iterations finished qdiffx linear iterations at : 19:17:02 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 9.4536963E-06 1.2798309E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 19:17:02 4.376u 0.258s 0:04.89 94.4% 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 19:17:02 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! 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: ZN5 556 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.860076 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): -32.22900 17.63400 ymin,ymax (A): -24.88500 21.89200 zmin,zma (A): -12.66800 44.74900 x,y,z range (A): 49.86300 46.77700 57.41700 scale (grids/A): 1.860076 object centre (A): -7.297500 -1.496500 16.04050 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 85.92371 87.73454 89.77783 assigned negative charge : -390.0956 centred at (gu) : 85.61163 87.82787 89.44090 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72514 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22087 grid for indexing accessible points = 1.400000 m= 26540 mr = 50908 m= 4129 mr = 20064 m= 227 mr = 2804 m= 0 mr = 94 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 7161 time to turn everything in is 0.5600000 number of dielectric boundary points 29540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 19335 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) : 0.6200255 object centre at (A) : -7.297500 -1.496500 16.04050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5681107E-02 2.2042010E-02 midg,1,midg; midg,igrid,midg 1.4263464E-02 2.1898581E-03 1,midg,midg; igrid,midg,midg -5.2872263E-03 3.8678333E-02 gauss-seidel spectral radius is 0.9985715 estimated iterations to convergence 210 setup time was (sec) 0.9000000 now iterating at: 19:17:03 rms-change max change #iterations 4.057716 190.5864 at 10iterations 1.865154 66.54565 at 20iterations 0.8576732 28.67852 at 30iterations 0.3947958 13.89256 at 40iterations 0.1820608 5.698483 at 50iterations 8.3937615E-02 2.523293 at 60iterations 3.8669858E-02 1.183105 at 70iterations 1.7758291E-02 0.5691113 at 80iterations 8.1625264E-03 0.2710876 at 90iterations 3.7774644E-03 0.1230221 at 100iterations 1.7357740E-03 5.7926178E-02 at 110iterations 8.0226880E-04 2.8549194E-02 at 120iterations finished qdiffx linear iterations at : 19:17:12 total time elapsed so far: 9.830000 # loops : 120 mean,max change (kT/e) : 8.0226880E-04 2.8549194E-02 energy calculations done at 9.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.01000 DelPhi exited at 19:17:13 10.015u 0.304s 0:10.62 97.0% 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 19:17:13 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2605 !!! 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: ZN5 556 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.790114 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): -32.22900 17.63400 ymin,ymax (A): -24.88500 21.89200 zmin,zma (A): -12.66800 44.74900 x,y,z range (A): 49.86300 46.77700 57.41700 scale (grids/A): 2.790114 object centre (A): -7.297500 -1.496500 16.04050 number of atom coordinates read : 2605 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 394.5950 centred at (gu) : 83.88538 86.60183 89.66656 assigned negative charge : -390.0956 centred at (gu) : 83.41737 86.74184 89.16127 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167537 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22087 grid for indexing accessible points = 1.400000 m= 86032 mr = 122856 m= 30992 mr = 71533 m= 7531 mr = 25381 m= 1077 mr = 6006 m= 49 mr = 771 m= 0 mr = 18 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 23812 time to turn everything in is 1.410000 number of dielectric boundary points 66653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19725 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) : 1.860076 object centre at (A) : -7.297500 -1.496500 16.04050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2450663E-02 0.2571942 midg,1,midg; midg,igrid,midg 0.1638454 -9.3174595E-03 1,midg,midg; igrid,midg,midg -3.2836929E-02 0.4746139 gauss-seidel spectral radius is 0.9992346 estimated iterations to convergence 285 setup time was (sec) 1.780000 now iterating at: 19:17:15 rms-change max change #iterations 9.469351 335.6913 at 10iterations 5.408739 112.2178 at 20iterations 3.076298 56.42855 at 30iterations 1.749731 31.33148 at 40iterations 0.9934509 21.81377 at 50iterations 0.5629872 10.79236 at 60iterations 0.3206165 5.720890 at 70iterations 0.1818049 3.327870 at 80iterations 0.1032719 1.952279 at 90iterations 5.8655702E-02 1.153336 at 100iterations 3.3327442E-02 0.6246243 at 110iterations 1.8935218E-02 0.3398690 at 120iterations 1.0749784E-02 0.2074966 at 130iterations 6.1143422E-03 0.1148567 at 140iterations 3.4695987E-03 6.3692093E-02 at 150iterations 1.9737489E-03 3.8684130E-02 at 160iterations 1.1190464E-03 2.3297787E-02 at 170iterations 6.3664338E-04 1.1698723E-02 at 180iterations finished qdiffx linear iterations at : 19:17:29 total time elapsed so far: 15.99000 # loops : 180 mean,max change (kT/e) : 6.3664338E-04 1.1698723E-02 energy calculations done at 15.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.18000 DelPhi exited at 19:17:30 16.181u 0.326s 0:16.78 98.3% 0+0k 0+0io 0pf+0w