Mon Oct 10 13:55:31 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+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 13:55:31 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 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: 0.5764902 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): -21.92900 39.82400 ymin,ymax (A): -9.697000 43.46100 zmin,zma (A): -1.654000 52.57000 x,y,z range (A): 61.75300 53.15800 54.22400 scale (grids/A): 0.5764902 object centre (A): 8.947501 16.88200 25.45800 number of atom coordinates read : 2706 total number of charged atoms : 2561 net assigned charge : 12.00002 assigned positive charge : 397.2641 centred at (gu) : 92.14449 90.53000 86.57835 assigned negative charge : -385.2646 centred at (gu) : 92.18798 90.55032 86.35117 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5914 nv = 96 ne = 84 npr = 52783 no. pairs analyzed = 52783 no. exposed pairs = 4051 no. arc points = 29029 no. surface atoms = 1345 nbur = 1361 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 259 mr = 2517 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2843 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7530 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5263170E-09 2.7775953E-09 midg,1,midg; midg,igrid,midg 2.4597013E-09 2.3732749E-09 1,midg,midg; igrid,midg,midg 1.9363975E-09 2.7917808E-09 gauss-seidel spectral radius is 0.9844615 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 13:55:32 rms-change max change #iterations 8.7287426E-02 18.42220 at 10iterations 6.6916924E-03 1.109447 at 20iterations 5.1628286E-04 8.6200714E-02 at 30iterations 4.4121782E-05 6.8244934E-03 at 40iterations 4.9904834E-06 6.8998337E-04 at 50iterations finished qdiffx linear iterations at : 13:55:35 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 4.9904834E-06 6.8998337E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 13:55:35 3.614u 0.212s 0:04.29 89.0% 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 Mon Oct 10 2011 at 13:55:35 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 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: 1.729471 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): -21.92900 39.82400 ymin,ymax (A): -9.697000 43.46100 zmin,zma (A): -1.654000 52.57000 x,y,z range (A): 61.75300 53.15800 54.22400 scale (grids/A): 1.729471 object centre (A): 8.947501 16.88200 25.45800 number of atom coordinates read : 2706 total number of charged atoms : 2561 net assigned charge : 12.00002 assigned positive charge : 397.2641 centred at (gu) : 96.43320 91.58947 79.73448 assigned negative charge : -385.2646 centred at (gu) : 96.56364 91.65057 79.05347 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29029 grid for indexing accessible points = 1.400000 m= 18496 mr = 37848 m= 2216 mr = 11516 m= 77 mr = 1005 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 33475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19843 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) : 0.5764902 object centre at (A) : 8.947501 16.88200 25.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2215071E-04 1.8452788E-02 midg,1,midg; midg,igrid,midg 1.9868612E-02 1.9824998E-02 1,midg,midg; igrid,midg,midg -1.1681007E-02 2.3172786E-02 gauss-seidel spectral radius is 0.9983629 estimated iterations to convergence 196 setup time was (sec) 0.8300000 now iterating at: 13:55:36 rms-change max change #iterations 3.483119 167.0255 at 10iterations 1.497728 70.16199 at 20iterations 0.6504333 25.39973 at 30iterations 0.2818115 12.08630 at 40iterations 0.1220839 4.360800 at 50iterations 5.2844923E-02 1.830643 at 60iterations 2.2991374E-02 0.8692951 at 70iterations 9.9862441E-03 0.3471775 at 80iterations 4.3234425E-03 0.1508446 at 90iterations 1.8845142E-03 6.7920685E-02 at 100iterations 8.1825990E-04 3.0206680E-02 at 110iterations 3.5579212E-04 1.3297081E-02 at 120iterations finished qdiffx linear iterations at : 13:55:43 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 3.5579212E-04 1.3297081E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 13:55:45 7.653u 0.257s 0:09.23 85.5% 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 13:55:45 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2706 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: 2.594206 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): -21.92900 39.82400 ymin,ymax (A): -9.697000 43.46100 zmin,zma (A): -1.654000 52.57000 x,y,z range (A): 61.75300 53.15800 54.22400 scale (grids/A): 2.594206 object centre (A): 8.947501 16.88200 25.45800 number of atom coordinates read : 2706 total number of charged atoms : 2561 net assigned charge : 12.00002 assigned positive charge : 397.2641 centred at (gu) : 99.64983 92.38403 74.60160 assigned negative charge : -385.2646 centred at (gu) : 99.84539 92.47591 73.58030 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 145809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29029 grid for indexing accessible points = 1.400000 m= 62461 mr = 94148 m= 18721 mr = 45900 m= 3441 mr = 13092 m= 302 mr = 2084 m= 13 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.200000 number of dielectric boundary points 75395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 20476 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) : 1.729471 object centre at (A) : 8.947501 16.88200 25.45800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9084001E-02 0.2063873 midg,1,midg; midg,igrid,midg 0.2947107 0.2476093 1,midg,midg; igrid,midg,midg -0.4936203 0.2470663 gauss-seidel spectral radius is 0.9991944 estimated iterations to convergence 278 setup time was (sec) 1.550000 now iterating at: 13:55:46 rms-change max change #iterations 8.992977 314.7148 at 10iterations 5.251725 144.6344 at 20iterations 3.028455 81.26627 at 30iterations 1.734027 48.91285 at 40iterations 0.9854212 23.37567 at 50iterations 0.5603989 14.20141 at 60iterations 0.3169687 7.444726 at 70iterations 0.1789399 4.568745 at 80iterations 0.1007777 2.392663 at 90iterations 5.6655429E-02 1.297985 at 100iterations 3.1913500E-02 0.6738901 at 110iterations 1.7927513E-02 0.4170537 at 120iterations 1.0062611E-02 0.2140301 at 130iterations 5.6399126E-03 0.1204243 at 140iterations 3.1684674E-03 7.3457718E-02 at 150iterations 1.7779217E-03 3.5987854E-02 at 160iterations 9.9845044E-04 2.1470070E-02 at 170iterations 5.5866770E-04 1.1815548E-02 at 180iterations finished qdiffx linear iterations at : 13:55:58 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 5.5866770E-04 1.1815548E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 13:55:58 13.096u 0.213s 0:13.63 97.5% 0+0k 0+0io 0pf+0w