Sat Oct 8 20:27:25 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 Sat Oct 8 2011 at 20:27:25 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 = 2567 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7243134 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): -6.312000 42.24400 ymin,ymax (A): -2.292000 46.85800 zmin,zma (A): -8.420000 39.91300 x,y,z range (A): 48.55600 49.15000 48.33300 scale (grids/A): 0.7243134 object centre (A): 17.96600 22.28300 15.74650 number of atom coordinates read : 2567 total number of charged atoms : 2441 net assigned charge : 3.500004 assigned positive charge : 387.6040 centred at (gu) : 88.33303 91.52718 90.83176 assigned negative charge : -384.1046 centred at (gu) : 88.22827 91.66316 90.72952 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8994 nv = 96 ne = 84 npr = 54018 no. pairs analyzed = 54018 no. exposed pairs = 2933 no. arc points = 21047 no. surface atoms = 980 nbur = 1587 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 591 mr = 5244 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 549 time to turn everything in is 0.3700000 number of dielectric boundary points 4204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1865 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6839051E-08 1.5835545E-07 midg,1,midg; midg,igrid,midg 1.2236823E-07 -1.0105868E-07 1,midg,midg; igrid,midg,midg -6.5178703E-08 9.9884915E-08 gauss-seidel spectral radius is 0.9901071 estimated iterations to convergence 82 setup time was (sec) 0.7000000 now iterating at: 20:27:26 rms-change max change #iterations 0.2496170 29.92270 at 10iterations 3.2941762E-02 3.676076 at 20iterations 4.2466410E-03 0.5536499 at 30iterations 5.5015908E-04 6.5835953E-02 at 40iterations 7.1818002E-05 1.0224342E-02 at 50iterations finished qdiffx linear iterations at : 20:27:30 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 7.1818002E-05 1.0224342E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 20:27:30 4.440u 0.309s 0:05.02 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 20:27:30 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 = 2567 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: 2.172940 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): -6.312000 42.24400 ymin,ymax (A): -2.292000 46.85800 zmin,zma (A): -8.420000 39.91300 x,y,z range (A): 48.55600 49.15000 48.33300 scale (grids/A): 2.172940 object centre (A): 17.96600 22.28300 15.74650 number of atom coordinates read : 2567 total number of charged atoms : 2441 net assigned charge : 3.500004 assigned positive charge : 387.6040 centred at (gu) : 84.99870 94.58119 92.49490 assigned negative charge : -384.1046 centred at (gu) : 84.68441 94.98911 92.18815 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 95943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21047 grid for indexing accessible points = 1.400000 m= 37887 mr = 68451 m= 7677 mr = 29418 m= 800 mr = 5482 m= 22 mr = 478 m= 0 mr = 1 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 14416 time to turn everything in is 0.7100000 number of dielectric boundary points 38499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 19434 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) : 0.7243134 object centre at (A) : 17.96600 22.28300 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5991979E-05 3.7502587E-02 midg,1,midg; midg,igrid,midg 1.0168818E-02 -7.4300945E-02 1,midg,midg; igrid,midg,midg -1.7313901E-02 0.1121408 gauss-seidel spectral radius is 0.9989170 estimated iterations to convergence 240 setup time was (sec) 1.050000 now iterating at: 20:27:31 rms-change max change #iterations 5.392183 216.7159 at 10iterations 2.736190 91.18800 at 20iterations 1.387674 39.56860 at 30iterations 0.7074435 20.25388 at 40iterations 0.3598650 9.542377 at 50iterations 0.1832587 4.863354 at 60iterations 9.3044832E-02 2.638092 at 70iterations 4.7472239E-02 1.251038 at 80iterations 2.4172034E-02 0.6670036 at 90iterations 1.2243420E-02 0.3063736 at 100iterations 6.2578302E-03 0.1663342 at 110iterations 3.1911051E-03 7.9071045E-02 at 120iterations finished qdiffx linear iterations at : 20:27:40 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 3.1911051E-03 7.9071045E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 20:27:40 9.845u 0.250s 0:10.41 96.9% 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 20:27:41 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 = 2567 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: 3.259410 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): -6.312000 42.24400 ymin,ymax (A): -2.292000 46.85800 zmin,zma (A): -8.420000 39.91300 x,y,z range (A): 48.55600 49.15000 48.33300 scale (grids/A): 3.259410 object centre (A): 17.96600 22.28300 15.74650 number of atom coordinates read : 2567 total number of charged atoms : 2441 net assigned charge : 3.500004 assigned positive charge : 387.6040 centred at (gu) : 82.49789 96.87142 93.74226 assigned negative charge : -384.1046 centred at (gu) : 82.02661 97.48346 93.28215 start vw surface at 0.1500000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 221189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21047 grid for indexing accessible points = 1.400000 m= 118019 mr = 164365 m= 48434 mr = 99612 m= 14909 mr = 40618 m= 3332 mr = 12056 m= 436 mr = 2606 m= 22 mr = 327 m= 0 mr = 4 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 48516 time to turn everything in is 2.340000 number of dielectric boundary points 86753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.500000 number of grid points assigned charge 19528 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) : 2.172940 object centre at (A) : 17.96600 22.28300 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2128233 0.2062415 midg,1,midg; midg,igrid,midg -5.2019380E-02 -0.5020724 1,midg,midg; igrid,midg,midg -0.1806062 1.652879 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 2.700000 now iterating at: 20:27:43 rms-change max change #iterations 11.67233 358.0515 at 10iterations 6.876639 134.0924 at 20iterations 4.054583 74.77100 at 30iterations 2.380311 36.95193 at 40iterations 1.402097 23.83397 at 50iterations 0.8278161 13.38232 at 60iterations 0.4872231 7.297709 at 70iterations 0.2866859 4.193123 at 80iterations 0.1686459 2.544468 at 90iterations 9.9362537E-02 1.562442 at 100iterations 5.8352876E-02 0.9030762 at 110iterations 3.4432121E-02 0.5753708 at 120iterations 2.0275915E-02 0.2918205 at 130iterations 1.1921539E-02 0.1854439 at 140iterations 7.0272950E-03 0.1048498 at 150iterations 4.1425452E-03 6.1596870E-02 at 160iterations 2.4430228E-03 3.9556503E-02 at 170iterations 1.4424897E-03 2.2745132E-02 at 180iterations finished qdiffx linear iterations at : 20:27:58 total time elapsed so far: 16.96000 # loops : 180 mean,max change (kT/e) : 1.4424897E-03 2.2745132E-02 energy calculations done at 16.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.14000 DelPhi exited at 20:27:58 17.142u 0.271s 0:17.69 98.4% 0+0k 0+0io 0pf+0w