Sun Oct 9 08:14:42 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 Sun Oct 9 2011 at 08:14:42 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: NDP 531 has a net charge of -3.0000 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: 0.6324953 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): 45.30000 101.5850 ymin,ymax (A): 26.98900 78.03100 zmin,zma (A): 13.43000 60.96100 x,y,z range (A): 56.28500 51.04200 47.53100 scale (grids/A): 0.6324953 object centre (A): 73.44250 52.51000 37.19550 number of atom coordinates read : 2755 total number of charged atoms : 2621 net assigned charge : 6.000007 assigned positive charge : 409.1926 centred at (gu) : 90.40695 89.56933 88.47906 assigned negative charge : -403.1934 centred at (gu) : 90.59516 89.55875 88.52876 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7498 nv = 96 ne = 84 npr = 56192 no. pairs analyzed = 56192 no. exposed pairs = 3351 no. arc points = 23582 no. surface atoms = 1134 nbur = 1621 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 4164 m= 0 mr = 32 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 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2285 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6505298E-08 1.6107825E-09 midg,1,midg; midg,igrid,midg 6.5509767E-09 7.3727002E-09 1,midg,midg; igrid,midg,midg 2.3029596E-08 -1.3011722E-08 gauss-seidel spectral radius is 0.9870677 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 08:14:43 rms-change max change #iterations 0.1427757 20.09966 at 10iterations 1.4005722E-02 2.187901 at 20iterations 1.3717900E-03 0.1929379 at 30iterations 1.4008956E-04 1.7316818E-02 at 40iterations 1.8149507E-05 2.3870468E-03 at 50iterations finished qdiffx linear iterations at : 08:14:46 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.8149507E-05 2.3870468E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 08:14:46 3.509u 0.221s 0:04.00 93.0% 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 Sun Oct 9 2011 at 08:14:46 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: NDP 531 has a net charge of -3.0000 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: 1.897486 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): 45.30000 101.5850 ymin,ymax (A): 26.98900 78.03100 zmin,zma (A): 13.43000 60.96100 x,y,z range (A): 56.28500 51.04200 47.53100 scale (grids/A): 1.897486 object centre (A): 73.44250 52.51000 37.19550 number of atom coordinates read : 2755 total number of charged atoms : 2621 net assigned charge : 6.000007 assigned positive charge : 409.1926 centred at (gu) : 91.22008 88.70751 85.43637 assigned negative charge : -403.1934 centred at (gu) : 91.78525 88.67603 85.58609 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23582 grid for indexing accessible points = 1.400000 m= 29985 mr = 57093 m= 4322 mr = 21841 m= 245 mr = 2418 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.5700000 number of dielectric boundary points 34443 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 20626 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) : 0.6324953 object centre at (A) : 73.44250 52.51000 37.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4468397E-02 -9.0894746E-03 midg,1,midg; midg,igrid,midg 1.0027900E-02 9.1528827E-03 1,midg,midg; igrid,midg,midg 6.6551507E-02 -5.0623096E-03 gauss-seidel spectral radius is 0.9986477 estimated iterations to convergence 215 setup time was (sec) 0.8700000 now iterating at: 08:14:47 rms-change max change #iterations 4.333599 214.6708 at 10iterations 2.034278 63.87100 at 20iterations 0.9524210 28.86785 at 30iterations 0.4485005 14.26066 at 40iterations 0.2107678 5.983410 at 50iterations 9.8862298E-02 2.986269 at 60iterations 4.6452310E-02 1.397284 at 70iterations 2.1865899E-02 0.6578783 at 80iterations 1.0260549E-02 0.3373871 at 90iterations 4.8387246E-03 0.1382160 at 100iterations 2.2795545E-03 7.1098328E-02 at 110iterations 1.0703850E-03 3.0900955E-02 at 120iterations finished qdiffx linear iterations at : 08:14:54 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.0703850E-03 3.0900955E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:14:55 8.003u 0.241s 0:08.54 96.4% 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 Sun Oct 9 2011 at 08:14:55 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2755 !!! WARNING: NDP 531 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.846229 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): 45.30000 101.5850 ymin,ymax (A): 26.98900 78.03100 zmin,zma (A): 13.43000 60.96100 x,y,z range (A): 56.28500 51.04200 47.53100 scale (grids/A): 2.846229 object centre (A): 73.44250 52.51000 37.19550 number of atom coordinates read : 2755 total number of charged atoms : 2621 net assigned charge : 6.000007 assigned positive charge : 409.1926 centred at (gu) : 91.82993 88.06116 83.15450 assigned negative charge : -403.1934 centred at (gu) : 92.67770 88.01393 83.37896 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 188272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23582 grid for indexing accessible points = 1.400000 m= 96668 mr = 138802 m= 35167 mr = 78593 m= 7506 mr = 27838 m= 1040 mr = 5201 m= 65 mr = 604 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 764 time to turn everything in is 1.470000 number of dielectric boundary points 77660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 20965 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) : 1.897486 object centre at (A) : 73.44250 52.51000 37.19550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1325270 -0.1257618 midg,1,midg; midg,igrid,midg 9.1885468E-03 7.5876988E-02 1,midg,midg; igrid,midg,midg 0.6476767 1.6490577E-02 gauss-seidel spectral radius is 0.9992713 estimated iterations to convergence 292 setup time was (sec) 1.810000 now iterating at: 08:14:57 rms-change max change #iterations 10.44439 399.1538 at 10iterations 6.227808 141.8862 at 20iterations 3.670342 81.14923 at 30iterations 2.157730 45.89851 at 40iterations 1.262581 30.41829 at 50iterations 0.7372255 14.06816 at 60iterations 0.4283625 7.812323 at 70iterations 0.2492870 4.494068 at 80iterations 0.1445809 2.866346 at 90iterations 8.3988704E-02 1.475075 at 100iterations 4.8607081E-02 0.8650513 at 110iterations 2.8132658E-02 0.4821930 at 120iterations 1.6288120E-02 0.2967777 at 130iterations 9.4201379E-03 0.1788654 at 140iterations 5.4384992E-03 9.4721794E-02 at 150iterations 3.1410169E-03 6.4582825E-02 at 160iterations 1.8169278E-03 3.1012297E-02 at 170iterations 1.0494872E-03 1.8049240E-02 at 180iterations finished qdiffx linear iterations at : 08:15:08 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 1.0494872E-03 1.8049240E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 08:15:09 13.385u 0.274s 0:14.00 97.5% 0+0k 0+0io 0pf+0w