Mon Oct 10 23:38:57 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 23:38:57 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 = 2824 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: 0.5533707 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): -24.49100 26.07100 ymin,ymax (A): -33.63100 22.15900 zmin,zma (A): -6.994000 57.33900 x,y,z range (A): 50.56200 55.79000 64.33300 scale (grids/A): 0.5533707 object centre (A): 0.7900000 -5.735998 25.17250 number of atom coordinates read : 2824 total number of charged atoms : 2742 net assigned charge : 1.000009 assigned positive charge : 417.6772 centred at (gu) : 91.43735 89.40977 91.11610 assigned negative charge : -416.6785 centred at (gu) : 91.30930 89.48322 91.02946 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5848 nv = 96 ne = 84 npr = 54612 no. pairs analyzed = 54612 no. exposed pairs = 3914 no. arc points = 27823 no. surface atoms = 1308 nbur = 1516 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 = 1.568000 m= 256 mr = 2814 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2872 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7591 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0017057E-10 9.9445530E-10 midg,1,midg; midg,igrid,midg 7.4976420E-10 -4.7501586E-10 1,midg,midg; igrid,midg,midg -7.0528772E-10 1.5495007E-09 gauss-seidel spectral radius is 0.9831607 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 23:38:58 rms-change max change #iterations 7.2300628E-02 12.86202 at 10iterations 4.9575018E-03 1.179607 at 20iterations 4.0856248E-04 6.3261986E-02 at 30iterations 5.3895626E-05 7.7075958E-03 at 40iterations 1.0663033E-05 1.3227463E-03 at 50iterations finished qdiffx linear iterations at : 23:39:01 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0663033E-05 1.3227463E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 23:39:02 3.390u 0.238s 0:04.29 84.3% 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 Mon Oct 10 2011 at 23:39:02 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 = 2824 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: 1.660112 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): -24.49100 26.07100 ymin,ymax (A): -33.63100 22.15900 zmin,zma (A): -6.994000 57.33900 x,y,z range (A): 50.56200 55.79000 64.33300 scale (grids/A): 1.660112 object centre (A): 0.7900000 -5.735998 25.17250 number of atom coordinates read : 2824 total number of charged atoms : 2742 net assigned charge : 1.000009 assigned positive charge : 417.6772 centred at (gu) : 94.31112 88.22858 93.34768 assigned negative charge : -416.6785 centred at (gu) : 93.92766 88.44967 93.08803 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19871 mr = 41481 m= 2226 mr = 13269 m= 63 mr = 1128 m= 0 mr = 10 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 30337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 305 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21188 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) : 0.5533707 object centre at (A) : 0.7900000 -5.735998 25.17250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2054385E-02 6.6397553E-03 midg,1,midg; midg,igrid,midg -1.2992398E-04 -9.7241988E-03 1,midg,midg; igrid,midg,midg -5.3824317E-03 1.9687358E-02 gauss-seidel spectral radius is 0.9982480 estimated iterations to convergence 190 setup time was (sec) 0.7900000 now iterating at: 23:39:03 rms-change max change #iterations 3.263512 145.9674 at 10iterations 1.373986 55.64908 at 20iterations 0.5809942 25.14969 at 30iterations 0.2451009 9.211821 at 40iterations 0.1037437 3.714860 at 50iterations 4.3732923E-02 1.607048 at 60iterations 1.8552408E-02 0.7081831 at 70iterations 7.8405645E-03 0.2888155 at 80iterations 3.3307730E-03 0.1263504 at 90iterations 1.4083873E-03 5.8216095E-02 at 100iterations 6.0158980E-04 2.0591736E-02 at 110iterations 2.6013330E-04 9.1550350E-03 at 120iterations finished qdiffx linear iterations at : 23:39:10 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 2.6013330E-04 9.1550350E-03 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 23:39:10 7.717u 0.251s 0:08.56 92.9% 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 Mon Oct 10 2011 at 23:39:10 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 = 2824 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: 2.490168 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): -24.49100 26.07100 ymin,ymax (A): -33.63100 22.15900 zmin,zma (A): -6.994000 57.33900 x,y,z range (A): 50.56200 55.79000 64.33300 scale (grids/A): 2.490168 object centre (A): 0.7900000 -5.735998 25.17250 number of atom coordinates read : 2824 total number of charged atoms : 2742 net assigned charge : 1.000009 assigned positive charge : 417.6772 centred at (gu) : 96.46665 87.34278 95.02148 assigned negative charge : -416.6785 centred at (gu) : 95.89147 87.67455 94.63200 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 148837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67509 mr = 102327 m= 20452 mr = 52219 m= 3456 mr = 15124 m= 245 mr = 2241 m= 11 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 68485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 21915 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) : 1.660112 object centre at (A) : 0.7900000 -5.735998 25.17250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5597470 0.1390521 midg,1,midg; midg,igrid,midg -4.9936257E-02 -0.1490327 1,midg,midg; igrid,midg,midg -0.1164767 0.2572625 gauss-seidel spectral radius is 0.9991646 estimated iterations to convergence 273 setup time was (sec) 1.430000 now iterating at: 23:39:12 rms-change max change #iterations 8.547039 379.4759 at 10iterations 4.864658 120.9499 at 20iterations 2.752307 62.53101 at 30iterations 1.556735 39.57166 at 40iterations 0.8742957 21.38890 at 50iterations 0.4888876 10.59149 at 60iterations 0.2725820 6.412537 at 70iterations 0.1524289 3.241913 at 80iterations 8.4942214E-02 1.948479 at 90iterations 4.7273852E-02 1.081553 at 100iterations 2.6281845E-02 0.5205421 at 110iterations 1.4630928E-02 0.3097878 at 120iterations 8.1223594E-03 0.1613665 at 130iterations 4.5166453E-03 9.7660065E-02 at 140iterations 2.5066657E-03 5.7830811E-02 at 150iterations 1.3969414E-03 3.4141302E-02 at 160iterations 7.7866577E-04 1.6372681E-02 at 170iterations 4.3614401E-04 9.3326569E-03 at 180iterations finished qdiffx linear iterations at : 23:39:23 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 4.3614401E-04 9.3326569E-03 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 23:39:23 12.376u 0.281s 0:12.98 97.4% 0+0k 0+0io 0pf+0w