Tue Oct 11 05:59:31 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 Tue Oct 11 2011 at 05:59:31 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6714700 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): 2.678000 47.80400 ymin,ymax (A): -26.73400 12.30500 zmin,zma (A): -2.819000 50.19900 x,y,z range (A): 45.12600 39.03900 53.01800 scale (grids/A): 0.6714700 object centre (A): 25.24100 -7.214500 23.69000 number of atom coordinates read : 2064 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.5771 centred at (gu) : 90.04830 90.29804 89.43474 assigned negative charge : -306.6461 centred at (gu) : 90.22520 90.27261 89.45079 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6234 nv = 96 ne = 84 npr = 41666 no. pairs analyzed = 41666 no. exposed pairs = 2464 no. arc points = 17061 no. surface atoms = 838 nbur = 1226 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 373 mr = 3546 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1666 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0525097E-08 1.8424700E-08 midg,1,midg; midg,igrid,midg 1.7560470E-08 3.1012522E-08 1,midg,midg; igrid,midg,midg 5.9582430E-08 -1.3843268E-08 gauss-seidel spectral radius is 0.9884486 estimated iterations to convergence 76 setup time was (sec) 0.3500000 now iterating at: 05:59:31 rms-change max change #iterations 0.1598096 25.69342 at 10iterations 1.7983176E-02 2.616486 at 20iterations 2.2918421E-03 0.3693695 at 30iterations 3.9419599E-04 5.3363800E-02 at 40iterations 9.6383330E-05 1.3561249E-02 at 50iterations finished qdiffx linear iterations at : 05:59:34 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 9.6383330E-05 1.3561249E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 05:59:35 3.325u 0.175s 0:04.09 85.3% 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 05:59:35 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.014410 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): 2.678000 47.80400 ymin,ymax (A): -26.73400 12.30500 zmin,zma (A): -2.819000 50.19900 x,y,z range (A): 45.12600 39.03900 53.01800 scale (grids/A): 2.014410 object centre (A): 25.24100 -7.214500 23.69000 number of atom coordinates read : 2064 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.5771 centred at (gu) : 90.14491 90.89428 88.30434 assigned negative charge : -306.6461 centred at (gu) : 90.67566 90.81796 88.35232 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17061 grid for indexing accessible points = 1.400000 m= 25517 mr = 47669 m= 4236 mr = 19111 m= 289 mr = 2617 m= 7 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 27784 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 15260 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) : 0.6714700 object centre at (A) : 25.24100 -7.214500 23.69000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0677387E-02 4.9492948E-02 midg,1,midg; midg,igrid,midg 3.4244910E-03 1.9550400E-02 1,midg,midg; igrid,midg,midg 3.2009490E-02 3.9706328E-03 gauss-seidel spectral radius is 0.9987147 estimated iterations to convergence 221 setup time was (sec) 0.5500000 now iterating at: 05:59:36 rms-change max change #iterations 4.164461 225.9202 at 10iterations 1.996905 69.19054 at 20iterations 0.9584118 32.52513 at 30iterations 0.4598564 17.16482 at 40iterations 0.2205943 7.246343 at 50iterations 0.1060617 3.370429 at 60iterations 5.0956648E-02 1.864464 at 70iterations 2.4506535E-02 0.7915649 at 80iterations 1.1904427E-02 0.4011345 at 90iterations 5.7862815E-03 0.2157593 at 100iterations 2.8416954E-03 9.9565506E-02 at 110iterations 1.4238203E-03 5.0432205E-02 at 120iterations finished qdiffx linear iterations at : 05:59:43 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.4238203E-03 5.0432205E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 05:59:43 7.660u 0.194s 0:08.45 92.8% 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 05:59:43 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.021615 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): 2.678000 47.80400 ymin,ymax (A): -26.73400 12.30500 zmin,zma (A): -2.819000 50.19900 x,y,z range (A): 45.12600 39.03900 53.01800 scale (grids/A): 3.021615 object centre (A): 25.24100 -7.214500 23.69000 number of atom coordinates read : 2064 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 313.5771 centred at (gu) : 90.21753 91.34132 87.45660 assigned negative charge : -306.6461 centred at (gu) : 91.01355 91.22684 87.52843 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17061 grid for indexing accessible points = 1.400000 m= 81973 mr = 114948 m= 30401 mr = 67821 m= 7760 mr = 24598 m= 1219 mr = 5745 m= 79 mr = 831 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 62674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 15448 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) : 2.014410 object centre at (A) : 25.24100 -7.214500 23.69000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2972325 0.6715866 midg,1,midg; midg,igrid,midg 1.4010661E-02 0.1657854 1,midg,midg; igrid,midg,midg 0.2584642 6.1977830E-02 gauss-seidel spectral radius is 0.9992641 estimated iterations to convergence 291 setup time was (sec) 1.110000 now iterating at: 05:59:45 rms-change max change #iterations 9.579348 521.2088 at 10iterations 5.594335 135.0205 at 20iterations 3.267117 65.83694 at 30iterations 1.894414 40.98527 at 40iterations 1.103189 21.30841 at 50iterations 0.6407164 12.94856 at 60iterations 0.3720323 7.038746 at 70iterations 0.2151666 4.506525 at 80iterations 0.1242656 2.432054 at 90iterations 7.2184645E-02 1.452602 at 100iterations 4.1790817E-02 0.8565063 at 110iterations 2.4365060E-02 0.4743423 at 120iterations 1.4284044E-02 0.2820759 at 130iterations 8.5110571E-03 0.1596069 at 140iterations 5.1584039E-03 9.8007202E-02 at 150iterations 3.2549102E-03 6.4711094E-02 at 160iterations 2.1555172E-03 4.0695429E-02 at 170iterations 1.5088494E-03 2.9586792E-02 at 180iterations finished qdiffx linear iterations at : 05:59:56 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 1.5088494E-03 2.9586792E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 05:59:56 12.245u 0.209s 0:13.01 95.6% 0+0k 0+0io 0pf+0w