Mon Oct 10 01:03:29 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+sph2.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 = amb2.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 01:03:29 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6418462 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): -5.300000 34.94800 ymin,ymax (A): -3.324000 47.79400 zmin,zma (A): -24.44000 31.02500 x,y,z range (A): 40.24800 51.11800 55.46500 scale (grids/A): 0.6418462 object centre (A): 14.82400 22.23500 3.292500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 90.58801 92.73131 90.24580 assigned negative charge : -288.8263 centred at (gu) : 90.69888 92.88190 90.20207 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5504 nv = 96 ne = 84 npr = 39959 no. pairs analyzed = 39959 no. exposed pairs = 2414 no. arc points = 16979 no. surface atoms = 817 nbur = 1147 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 3149 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.1600000 number of dielectric boundary points 2596 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1720 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0422868E-09 9.4703454E-09 midg,1,midg; midg,igrid,midg 1.0363316E-08 -1.6361266E-08 1,midg,midg; igrid,midg,midg 1.3193924E-08 -5.8185616E-09 gauss-seidel spectral radius is 0.9873659 estimated iterations to convergence 73 setup time was (sec) 0.3500000 now iterating at: 01:03:30 rms-change max change #iterations 0.1247466 20.81372 at 10iterations 1.2746627E-02 1.917824 at 20iterations 1.2407509E-03 0.1928657 at 30iterations 1.2426848E-04 2.0077705E-02 at 40iterations 1.2366454E-05 1.8424988E-03 at 50iterations finished qdiffx linear iterations at : 01:03:33 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.2366454E-05 1.8424988E-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) 3.350000 DelPhi exited at 01:03:33 3.358u 0.176s 0:03.79 92.8% 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 01:03:33 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.925539 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): -5.300000 34.94800 ymin,ymax (A): -3.324000 47.79400 zmin,zma (A): -24.44000 31.02500 x,y,z range (A): 40.24800 51.11800 55.46500 scale (grids/A): 1.925539 object centre (A): 14.82400 22.23500 3.292500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 91.76402 98.19402 90.73734 assigned negative charge : -288.8263 centred at (gu) : 92.09687 98.64575 90.60619 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 22350 mr = 41320 m= 3495 mr = 17377 m= 196 mr = 2363 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 2215 time to turn everything in is 0.3000000 number of dielectric boundary points 24210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14472 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) : 0.6418462 object centre at (A) : 14.82400 22.23500 3.292500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5163106E-02 1.2293196E-02 midg,1,midg; midg,igrid,midg 3.2804947E-02 -9.1094067E-03 1,midg,midg; igrid,midg,midg 1.0671994E-02 -4.3542087E-03 gauss-seidel spectral radius is 0.9985833 estimated iterations to convergence 211 setup time was (sec) 0.5100000 now iterating at: 01:03:34 rms-change max change #iterations 3.718539 180.8238 at 10iterations 1.717562 66.01112 at 20iterations 0.7966218 29.31165 at 30iterations 0.3681859 13.44887 at 40iterations 0.1694772 5.832086 at 50iterations 7.8188702E-02 3.194763 at 60iterations 3.6086798E-02 1.337422 at 70iterations 1.6663291E-02 0.5440044 at 80iterations 7.6969294E-03 0.2590494 at 90iterations 3.5513872E-03 0.1239767 at 100iterations 1.6464755E-03 5.5459976E-02 at 110iterations 7.5963419E-04 2.6854515E-02 at 120iterations finished qdiffx linear iterations at : 01:03:41 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 7.5963419E-04 2.6854515E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 01:03:41 7.692u 0.202s 0:08.25 95.6% 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 01:03:42 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.888308 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): -5.300000 34.94800 ymin,ymax (A): -3.324000 47.79400 zmin,zma (A): -24.44000 31.02500 x,y,z range (A): 40.24800 51.11800 55.46500 scale (grids/A): 2.888308 object centre (A): 14.82400 22.23500 3.292500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.8259 centred at (gu) : 92.64610 102.2910 91.10599 assigned negative charge : -288.8263 centred at (gu) : 93.14533 102.9688 90.90929 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 137192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16979 grid for indexing accessible points = 1.400000 m= 71623 mr = 99913 m= 26850 mr = 59979 m= 6151 mr = 22619 m= 855 mr = 4861 m= 58 mr = 641 m= 0 mr = 32 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 7824 time to turn everything in is 0.7800000 number of dielectric boundary points 54684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14656 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) : 1.925539 object centre at (A) : 14.82400 22.23500 3.292500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.084933 -1.2941864E-02 midg,1,midg; midg,igrid,midg 0.3692258 -0.1393100 1,midg,midg; igrid,midg,midg 7.4583225E-02 -1.8177120E-02 gauss-seidel spectral radius is 0.9992299 estimated iterations to convergence 284 setup time was (sec) 1.000000 now iterating at: 01:03:43 rms-change max change #iterations 8.660598 366.3768 at 10iterations 4.959615 112.0686 at 20iterations 2.819397 61.71125 at 30iterations 1.598778 32.60312 at 40iterations 0.9083637 17.14967 at 50iterations 0.5143564 10.47812 at 60iterations 0.2921096 5.638401 at 70iterations 0.1655895 3.269057 at 80iterations 9.3729131E-02 1.995935 at 90iterations 5.3189754E-02 1.060289 at 100iterations 3.0030506E-02 0.6176956 at 110iterations 1.7094687E-02 0.3563118 at 120iterations 9.6802143E-03 0.2008667 at 130iterations 5.4932293E-03 0.1067429 at 140iterations 3.1103892E-03 6.0793877E-02 at 150iterations 1.7648468E-03 3.3100128E-02 at 160iterations 1.0015232E-03 1.9699574E-02 at 170iterations 5.6774012E-04 1.1662960E-02 at 180iterations finished qdiffx linear iterations at : 01:03:54 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 5.6774012E-04 1.1662960E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.22000 DelPhi exited at 01:03:54 12.222u 0.215s 0:12.74 97.5% 0+0k 0+0io 0pf+0w