Wed Dec 21 14:21:05 PST 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 Wed Dec 21 2011 at 14:21:05 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASH 122 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6110644 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): -23.68800 34.57100 ymin,ymax (A): -18.36000 20.52300 zmin,zma (A): -3.689000 38.37000 x,y,z range (A): 58.25900 38.88300 42.05900 scale (grids/A): 0.6110644 object centre (A): 5.441502 1.081500 17.34050 number of atom coordinates read : 1990 total number of charged atoms : 1857 net assigned charge : 1.681007 assigned positive charge : 293.5739 centred at (gu) : 89.83793 90.02537 90.23840 assigned negative charge : -291.8933 centred at (gu) : 89.85352 90.12559 90.40678 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5083 nv = 96 ne = 84 npr = 39669 no. pairs analyzed = 39669 no. exposed pairs = 2618 no. arc points = 18004 no. surface atoms = 892 nbur = 1098 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 259 mr = 2664 m= 0 mr = 20 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 2658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1823 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6071 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0164035E-09 -5.8610845E-09 midg,1,midg; midg,igrid,midg 4.8342392E-09 -2.8627103E-09 1,midg,midg; igrid,midg,midg 1.7105850E-09 4.3687398E-10 gauss-seidel spectral radius is 0.9860852 estimated iterations to convergence 69 setup time was (sec) 0.4900000 now iterating at: 14:21:06 rms-change max change #iterations 0.1007333 18.56477 at 10iterations 8.7961489E-03 1.562084 at 20iterations 7.7503506E-04 0.1236296 at 30iterations 6.8363901E-05 1.1482239E-02 at 40iterations 6.0238031E-06 9.0789795E-04 at 50iterations finished qdiffx linear iterations at : 14:21:10 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 6.0238031E-06 9.0789795E-04 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 14:21:11 4.435u 0.441s 0:05.37 90.6% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:11 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASH 122 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.833193 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): -23.68800 34.57100 ymin,ymax (A): -18.36000 20.52300 zmin,zma (A): -3.689000 38.37000 x,y,z range (A): 58.25900 38.88300 42.05900 scale (grids/A): 1.833193 object centre (A): 5.441502 1.081500 17.34050 number of atom coordinates read : 1990 total number of charged atoms : 1857 net assigned charge : 1.681007 assigned positive charge : 293.5739 centred at (gu) : 89.51379 90.07610 90.71530 assigned negative charge : -291.8933 centred at (gu) : 89.56085 90.37698 91.22064 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 54134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18004 grid for indexing accessible points = 1.400000 m= 19683 mr = 36424 m= 2845 mr = 14421 m= 118 mr = 1687 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 24220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 14562 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) : 0.6110644 object centre at (A) : 5.441502 1.081500 17.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0927638E-03 -9.9352906E-03 midg,1,midg; midg,igrid,midg 2.4627990E-03 -4.9806265E-03 1,midg,midg; igrid,midg,midg 4.3431539E-02 3.4123767E-02 gauss-seidel spectral radius is 0.9984602 estimated iterations to convergence 202 setup time was (sec) 0.7400000 now iterating at: 14:21:12 rms-change max change #iterations 3.332393 156.0880 at 10iterations 1.479997 57.73948 at 20iterations 0.6615291 27.00657 at 30iterations 0.2944959 11.23147 at 40iterations 0.1309066 5.296989 at 50iterations 5.8786295E-02 2.413780 at 60iterations 2.6147112E-02 0.9908826 at 70iterations 1.1664690E-02 0.4191504 at 80iterations 5.1895739E-03 0.1902790 at 90iterations 2.3303849E-03 8.3378315E-02 at 100iterations 1.0381346E-03 3.7378311E-02 at 110iterations 4.6443852E-04 1.8726349E-02 at 120iterations finished qdiffx linear iterations at : 14:21:21 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 4.6443852E-04 1.8726349E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.24000 DelPhi exited at 14:21:26 10.243u 0.473s 0:15.19 70.5% 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 Wed Dec 21 2011 at 14:21:26 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASH 122 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.749790 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): -23.68800 34.57100 ymin,ymax (A): -18.36000 20.52300 zmin,zma (A): -3.689000 38.37000 x,y,z range (A): 58.25900 38.88300 42.05900 scale (grids/A): 2.749790 object centre (A): 5.441502 1.081500 17.34050 number of atom coordinates read : 1990 total number of charged atoms : 1857 net assigned charge : 1.681007 assigned positive charge : 293.5739 centred at (gu) : 89.27069 90.11407 91.07288 assigned negative charge : -291.8933 centred at (gu) : 89.34135 90.56538 91.83105 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 124691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18004 grid for indexing accessible points = 1.400000 m= 63530 mr = 88163 m= 22735 mr = 51642 m= 4937 mr = 18102 m= 475 mr = 3612 m= 16 mr = 246 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 54616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14854 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) : 1.833193 object centre at (A) : 5.441502 1.081500 17.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8050817E-02 -9.7408719E-02 midg,1,midg; midg,igrid,midg -5.0414237E-03 -4.3203335E-02 1,midg,midg; igrid,midg,midg 0.5214912 0.4166528 gauss-seidel spectral radius is 0.9991961 estimated iterations to convergence 278 setup time was (sec) 1.950000 now iterating at: 14:21:29 rms-change max change #iterations 8.222247 333.2362 at 10iterations 4.753365 126.3516 at 20iterations 2.707731 68.78809 at 30iterations 1.546465 36.15265 at 40iterations 0.8762047 20.57407 at 50iterations 0.4958540 11.97921 at 60iterations 0.2801863 5.815921 at 70iterations 0.1577857 4.027557 at 80iterations 8.8896684E-02 1.830074 at 90iterations 5.0063811E-02 1.097324 at 100iterations 2.8103709E-02 0.5874062 at 110iterations 1.5818344E-02 0.3436909 at 120iterations 8.9029865E-03 0.1927922 at 130iterations 4.9880259E-03 9.9370956E-02 at 140iterations 2.7978392E-03 5.8300972E-02 at 150iterations 1.5727794E-03 3.3143997E-02 at 160iterations 8.8203338E-04 1.9287109E-02 at 170iterations 4.9497775E-04 1.0334969E-02 at 180iterations finished qdiffx linear iterations at : 14:21:54 total time elapsed so far: 26.31000 # loops : 180 mean,max change (kT/e) : 4.9497775E-04 1.0334969E-02 energy calculations done at 26.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.52000 DelPhi exited at 14:22:05 26.527u 0.827s 0:38.74 70.5% 0+0k 0+0io 0pf+0w