Mon Oct 10 17:03:14 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 Mon Oct 10 2011 at 17:03:14 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 = 2843 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.6338467 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): -24.77800 31.38700 ymin,ymax (A): 3.741000 50.81100 zmin,zma (A): 0.3750001 55.15800 x,y,z range (A): 56.16500 47.07000 54.78300 scale (grids/A): 0.6338467 object centre (A): 3.304501 27.27600 27.76650 number of atom coordinates read : 2843 total number of charged atoms : 2702 net assigned charge : -2.999965 assigned positive charge : 426.8642 centred at (gu) : 90.55649 90.38069 88.70978 assigned negative charge : -429.8653 centred at (gu) : 90.66343 90.54295 88.61382 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7816 nv = 96 ne = 84 npr = 56146 no. pairs analyzed = 56146 no. exposed pairs = 3823 no. arc points = 26441 no. surface atoms = 1290 nbur = 1553 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4137 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3800000 number of dielectric boundary points 4047 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2616 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9308 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8400119E-08 5.2491607E-09 midg,1,midg; midg,igrid,midg 1.2885588E-08 -2.3145452E-08 1,midg,midg; igrid,midg,midg 7.2200157E-09 -1.7042986E-08 gauss-seidel spectral radius is 0.9871353 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 17:03:15 rms-change max change #iterations 0.1449113 20.38217 at 10iterations 1.3900961E-02 1.916237 at 20iterations 1.3490511E-03 0.1937752 at 30iterations 1.3319352E-04 1.6944885E-02 at 40iterations 1.4104891E-05 2.5405884E-03 at 50iterations finished qdiffx linear iterations at : 17:03:18 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 1.4104891E-05 2.5405884E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 17:03:20 3.949u 0.171s 0:05.50 74.7% 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 Mon Oct 10 2011 at 17:03:20 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 = 2843 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: 1.901540 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): -24.77800 31.38700 ymin,ymax (A): 3.741000 50.81100 zmin,zma (A): 0.3750001 55.15800 x,y,z range (A): 56.16500 47.07000 54.78300 scale (grids/A): 1.901540 object centre (A): 3.304501 27.27600 27.76650 number of atom coordinates read : 2843 total number of charged atoms : 2702 net assigned charge : -2.999965 assigned positive charge : 426.8642 centred at (gu) : 91.66874 91.14140 86.12847 assigned negative charge : -429.8653 centred at (gu) : 91.99001 91.62845 85.84116 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 83680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26441 grid for indexing accessible points = 1.400000 m= 29185 mr = 56627 m= 4197 mr = 20855 m= 237 mr = 2425 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 315 time to turn everything in is 0.6800000 number of dielectric boundary points 37315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 210 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21299 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) : 0.6338467 object centre at (A) : 3.304501 27.27600 27.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5144525E-04 8.3039729E-03 midg,1,midg; midg,igrid,midg 9.1500897E-03 -3.3398349E-02 1,midg,midg; igrid,midg,midg 2.9198006E-02 -6.7387410E-02 gauss-seidel spectral radius is 0.9986627 estimated iterations to convergence 217 setup time was (sec) 1.010000 now iterating at: 17:03:21 rms-change max change #iterations 4.461635 175.8202 at 10iterations 2.097094 77.18034 at 20iterations 0.9866570 28.69395 at 30iterations 0.4658173 14.69175 at 40iterations 0.2192091 6.700001 at 50iterations 0.1034436 3.368879 at 60iterations 4.8768405E-02 1.454681 at 70iterations 2.2931384E-02 0.6932297 at 80iterations 1.0824568E-02 0.2934990 at 90iterations 5.0766408E-03 0.1558247 at 100iterations 2.4054635E-03 8.3278656E-02 at 110iterations 1.1340010E-03 3.1877518E-02 at 120iterations finished qdiffx linear iterations at : 17:03:28 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 1.1340010E-03 3.1877518E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 17:03:31 8.460u 0.258s 0:11.24 77.4% 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 Mon Oct 10 2011 at 17:03:31 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 = 2843 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.852310 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): -24.77800 31.38700 ymin,ymax (A): 3.741000 50.81100 zmin,zma (A): 0.3750001 55.15800 x,y,z range (A): 56.16500 47.07000 54.78300 scale (grids/A): 2.852310 object centre (A): 3.304501 27.27600 27.76650 number of atom coordinates read : 2843 total number of charged atoms : 2702 net assigned charge : -2.999965 assigned positive charge : 426.8642 centred at (gu) : 92.50288 91.71188 84.19253 assigned negative charge : -429.8653 centred at (gu) : 92.98511 92.44254 83.76173 start vw surface at 0.2100000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 193583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26441 grid for indexing accessible points = 1.400000 m= 95181 mr = 137684 m= 33195 mr = 76406 m= 7474 mr = 26084 m= 935 mr = 5272 m= 56 mr = 582 m= 0 mr = 16 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 1192 time to turn everything in is 1.630000 number of dielectric boundary points 84380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 21616 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) : 1.901540 object centre at (A) : 3.304501 27.27600 27.76650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2540317 -0.1852791 midg,1,midg; midg,igrid,midg 5.6532208E-02 -0.2933831 1,midg,midg; igrid,midg,midg 0.4667698 -0.7576329 gauss-seidel spectral radius is 0.9992866 estimated iterations to convergence 295 setup time was (sec) 1.960000 now iterating at: 17:03:34 rms-change max change #iterations 10.58446 410.1582 at 10iterations 6.303692 134.3751 at 20iterations 3.717459 80.07037 at 30iterations 2.189732 47.71525 at 40iterations 1.283561 24.03907 at 50iterations 0.7500408 13.59702 at 60iterations 0.4384085 8.305645 at 70iterations 0.2554017 4.567576 at 80iterations 0.1490133 2.622722 at 90iterations 8.6451434E-02 1.688161 at 100iterations 5.0421238E-02 0.8258972 at 110iterations 2.9329324E-02 0.5355234 at 120iterations 1.7041646E-02 0.2970695 at 130iterations 9.8843938E-03 0.1662483 at 140iterations 5.7437788E-03 0.1050367 at 150iterations 3.3348380E-03 5.5923462E-02 at 160iterations 1.9384987E-03 3.2876015E-02 at 170iterations 1.1259909E-03 1.9910812E-02 at 180iterations finished qdiffx linear iterations at : 17:03:45 total time elapsed so far: 13.05000 # loops : 180 mean,max change (kT/e) : 1.1259909E-03 1.9910812E-02 energy calculations done at 13.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 17:03:46 13.272u 0.270s 0:15.03 90.0% 0+0k 0+0io 0pf+0w