Wed Dec 21 14:21:45 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+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 Wed Dec 21 2011 at 14:21:45 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1918 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 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: 0.6442739 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): -4.651000 35.29300 ymin,ymax (A): -3.750000 48.58200 zmin,zma (A): -24.02100 31.23500 x,y,z range (A): 39.94400 52.33200 55.25600 scale (grids/A): 0.6442739 object centre (A): 15.32100 22.41600 3.607000 number of atom coordinates read : 1918 total number of charged atoms : 1786 net assigned charge : -2.574996 assigned positive charge : 280.3330 centred at (gu) : 90.42446 92.68633 89.95380 assigned negative charge : -282.9083 centred at (gu) : 90.52084 92.85757 89.90771 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5648 nv = 96 ne = 84 npr = 38915 no. pairs analyzed = 38915 no. exposed pairs = 2409 no. arc points = 16886 no. surface atoms = 818 nbur = 1100 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 346 mr = 3235 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1700000 number of dielectric boundary points 2715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1616 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1032239E-09 6.8157768E-10 midg,1,midg; midg,igrid,midg 6.8348984E-09 -3.6210036E-08 1,midg,midg; igrid,midg,midg 4.8822990E-09 -1.4073955E-08 gauss-seidel spectral radius is 0.9874610 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 14:21:47 rms-change max change #iterations 0.1288567 19.92497 at 10iterations 1.2999937E-02 1.939468 at 20iterations 1.2798137E-03 0.1876297 at 30iterations 1.2921628E-04 2.0667076E-02 at 40iterations 1.2923047E-05 2.1953583E-03 at 50iterations finished qdiffx linear iterations at : 14:21:51 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 1.2923047E-05 2.1953583E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 14:22:22 4.502u 0.386s 0:37.37 13.0% 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 Wed Dec 21 2011 at 14:22:24 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1918 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 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: 1.932822 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): -4.651000 35.29300 ymin,ymax (A): -3.750000 48.58200 zmin,zma (A): -24.02100 31.23500 x,y,z range (A): 39.94400 52.33200 55.25600 scale (grids/A): 1.932822 object centre (A): 15.32100 22.41600 3.607000 number of atom coordinates read : 1918 total number of charged atoms : 1786 net assigned charge : -2.574996 assigned positive charge : 280.3330 centred at (gu) : 91.27349 98.05891 89.86145 assigned negative charge : -282.9083 centred at (gu) : 91.56269 98.57290 89.72331 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 59786 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 24661 mr = 41556 m= 4356 mr = 19523 m= 262 mr = 2970 m= 3 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1171 time to turn everything in is 0.3800000 number of dielectric boundary points 24892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14085 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) : 0.6442739 object centre at (A) : 15.32100 22.41600 3.607000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4877964E-03 -2.0995701E-03 midg,1,midg; midg,igrid,midg 2.5598969E-02 -2.5230795E-02 1,midg,midg; igrid,midg,midg 1.8734797E-03 -6.4256284E-03 gauss-seidel spectral radius is 0.9985964 estimated iterations to convergence 212 setup time was (sec) 0.8400000 now iterating at: 14:22:26 rms-change max change #iterations 3.666421 167.6339 at 10iterations 1.693345 62.87336 at 20iterations 0.7881179 26.91778 at 30iterations 0.3666321 12.94663 at 40iterations 0.1696186 5.770874 at 50iterations 7.8196846E-02 2.511269 at 60iterations 3.6371008E-02 1.229414 at 70iterations 1.6828166E-02 0.5990391 at 80iterations 7.8011178E-03 0.2573962 at 90iterations 3.6076491E-03 0.1213214 at 100iterations 1.6745775E-03 6.1431885E-02 at 110iterations 7.7858637E-04 3.0508995E-02 at 120iterations finished qdiffx linear iterations at : 14:22:36 total time elapsed so far: 10.48000 # loops : 120 mean,max change (kT/e) : 7.7858637E-04 3.0508995E-02 energy calculations done at 10.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 14:22:48 10.642u 0.478s 0:23.62 47.0% 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 Wed Dec 21 2011 at 14:22:49 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1918 !!! WARNING: LYS 7 has a net charge of 0.0730 !!! WARNING: LYS 14 has a net charge of 0.0730 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 106 has a net charge of 0.0730 !!! WARNING: LYS 142 has a net charge of 0.0730 !!! WARNING: LYS 169 has a net charge of 0.0730 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: 2.899233 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): -4.651000 35.29300 ymin,ymax (A): -3.750000 48.58200 zmin,zma (A): -24.02100 31.23500 x,y,z range (A): 39.94400 52.33200 55.25600 scale (grids/A): 2.899233 object centre (A): 15.32100 22.41600 3.607000 number of atom coordinates read : 1918 total number of charged atoms : 1786 net assigned charge : -2.574996 assigned positive charge : 280.3330 centred at (gu) : 91.91016 102.0883 89.79227 assigned negative charge : -282.9083 centred at (gu) : 92.34411 102.8594 89.58497 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 137684 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16886 grid for indexing accessible points = 1.400000 m= 75978 mr = 99879 m= 31646 mr = 64281 m= 8075 mr = 27029 m= 1154 mr = 6363 m= 96 mr = 877 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 3921 time to turn everything in is 0.9900000 number of dielectric boundary points 56160 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 14288 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) : 1.932822 object centre at (A) : 15.32100 22.41600 3.607000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4594141 -9.2893228E-02 midg,1,midg; midg,igrid,midg 0.2556990 -0.2687095 1,midg,midg; igrid,midg,midg 1.1107960E-02 -3.5515144E-02 gauss-seidel spectral radius is 0.9992344 estimated iterations to convergence 285 setup time was (sec) 1.460000 now iterating at: 14:22:51 rms-change max change #iterations 8.565487 468.0083 at 10iterations 4.896507 118.7391 at 20iterations 2.793834 77.96087 at 30iterations 1.586197 35.93326 at 40iterations 0.9060864 20.99894 at 50iterations 0.5155451 13.18952 at 60iterations 0.2934165 7.899010 at 70iterations 0.1667455 3.620618 at 80iterations 9.4668783E-02 1.954879 at 90iterations 5.3807802E-02 1.249613 at 100iterations 3.0494126E-02 0.6507287 at 110iterations 1.7357502E-02 0.4024181 at 120iterations 9.8707238E-03 0.2081246 at 130iterations 5.6026876E-03 0.1114712 at 140iterations 3.1922783E-03 6.4319611E-02 at 150iterations 1.8085336E-03 3.6003113E-02 at 160iterations 1.0270784E-03 1.9815445E-02 at 170iterations 5.8314926E-04 1.1291504E-02 at 180iterations finished qdiffx linear iterations at : 14:23:07 total time elapsed so far: 17.50000 # loops : 180 mean,max change (kT/e) : 5.8314926E-04 1.1291504E-02 energy calculations done at 17.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.64000 DelPhi exited at 14:23:09 17.640u 0.627s 0:20.04 91.1% 0+0k 0+0io 0pf+0w