Sat Oct 8 11:32:54 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 Sat Oct 8 2011 at 11:32:54 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 = 4396 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: 0.5587206 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): -25.12100 35.10500 ymin,ymax (A): 34.94600 98.66300 zmin,zma (A): 31.13300 89.11200 x,y,z range (A): 60.22600 63.71700 57.97900 scale (grids/A): 0.5587206 object centre (A): 4.992000 66.80450 60.12250 number of atom coordinates read : 4396 total number of charged atoms : 4245 net assigned charge : -1.999943 assigned positive charge : 662.0641 centred at (gu) : 90.80958 88.37173 88.89505 assigned negative charge : -664.0673 centred at (gu) : 90.65806 88.50734 89.04538 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8749 nv = 96 ne = 84 npr = 92690 no. pairs analyzed = 92690 no. exposed pairs = 4882 no. arc points = 33441 no. surface atoms = 1654 nbur = 2742 mkacc time = 0.1700000 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 = 1.540000 m= 355 mr = 5100 m= 0 mr = 37 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.3100000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3431 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6842841E-09 -2.0605422E-09 midg,1,midg; midg,igrid,midg 2.7267304E-09 -1.6541980E-09 1,midg,midg; igrid,midg,midg -2.2298761E-09 2.5149518E-09 gauss-seidel spectral radius is 0.9835740 estimated iterations to convergence 64 setup time was (sec) 0.5100000 now iterating at: 11:32:54 rms-change max change #iterations 9.9541470E-02 14.64941 at 10iterations 7.3333150E-03 0.9123402 at 20iterations 6.7308539E-04 8.8022232E-02 at 30iterations 1.3262359E-04 1.7192066E-02 at 40iterations 4.0228555E-05 5.5949688E-03 at 50iterations finished qdiffx linear iterations at : 11:32:57 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 4.0228555E-05 5.5949688E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 11:32:58 3.698u 0.207s 0:04.23 91.9% 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 Sat Oct 8 2011 at 11:32:58 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 = 4396 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: 1.676162 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): -25.12100 35.10500 ymin,ymax (A): 34.94600 98.66300 zmin,zma (A): 31.13300 89.11200 x,y,z range (A): 60.22600 63.71700 57.97900 scale (grids/A): 1.676162 object centre (A): 4.992000 66.80450 60.12250 number of atom coordinates read : 4396 total number of charged atoms : 4245 net assigned charge : -1.999943 assigned positive charge : 662.0641 centred at (gu) : 92.42770 85.11383 86.68391 assigned negative charge : -664.0673 centred at (gu) : 91.97368 85.52174 87.13566 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 98393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33441 grid for indexing accessible points = 1.400000 m= 31718 mr = 71675 m= 3697 mr = 23168 m= 105 mr = 2216 m= 0 mr = 24 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 6678 time to turn everything in is 0.4700000 number of dielectric boundary points 36830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 364 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 32695 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) : 0.5587206 object centre at (A) : 4.992000 66.80450 60.12250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0869573E-02 -2.2923620E-02 midg,1,midg; midg,igrid,midg 3.0037234E-02 -7.5328276E-03 1,midg,midg; igrid,midg,midg -1.8591123E-02 3.0969938E-02 gauss-seidel spectral radius is 0.9984053 estimated iterations to convergence 199 setup time was (sec) 0.7000000 now iterating at: 11:32:59 rms-change max change #iterations 4.392919 183.9095 at 10iterations 1.935419 60.96465 at 20iterations 0.8571371 26.65140 at 30iterations 0.3789391 10.62422 at 40iterations 0.1669655 5.645126 at 50iterations 7.3655568E-02 2.035465 at 60iterations 3.2479599E-02 0.9343648 at 70iterations 1.4438850E-02 0.4044130 at 80iterations 6.4035398E-03 0.1892996 at 90iterations 2.8437136E-03 8.6196899E-02 at 100iterations 1.2805969E-03 3.7162781E-02 at 110iterations 5.8924698E-04 1.7780304E-02 at 120iterations finished qdiffx linear iterations at : 11:33:06 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 5.8924698E-04 1.7780304E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 11:33:07 8.444u 0.251s 0:09.04 96.1% 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 Sat Oct 8 2011 at 11:33:07 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 = 4396 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: 2.514243 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): -25.12100 35.10500 ymin,ymax (A): 34.94600 98.66300 zmin,zma (A): 31.13300 89.11200 x,y,z range (A): 60.22600 63.71700 57.97900 scale (grids/A): 2.514243 object centre (A): 4.992000 66.80450 60.12250 number of atom coordinates read : 4396 total number of charged atoms : 4245 net assigned charge : -1.999943 assigned positive charge : 662.0641 centred at (gu) : 93.64120 82.67063 85.02561 assigned negative charge : -664.0673 centred at (gu) : 92.96035 83.28251 85.70338 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 229119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33441 grid for indexing accessible points = 1.400000 m= 109920 mr = 174125 m= 32545 mr = 90400 m= 6203 mr = 25764 m= 581 mr = 4615 m= 16 mr = 345 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 22497 time to turn everything in is 1.210000 number of dielectric boundary points 83135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 33938 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) : 1.676162 object centre at (A) : 4.992000 66.80450 60.12250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6003262 -0.2971421 midg,1,midg; midg,igrid,midg 0.4504273 -4.4762930E-03 1,midg,midg; igrid,midg,midg -0.2543618 0.3428881 gauss-seidel spectral radius is 0.9992218 estimated iterations to convergence 283 setup time was (sec) 1.490000 now iterating at: 11:33:09 rms-change max change #iterations 11.03771 320.9785 at 10iterations 6.359341 130.7808 at 20iterations 3.656277 67.17110 at 30iterations 2.087305 38.05925 at 40iterations 1.191624 22.72932 at 50iterations 0.6789474 12.59486 at 60iterations 0.3873807 7.151659 at 70iterations 0.2202506 3.490742 at 80iterations 0.1250480 2.061159 at 90iterations 7.0966490E-02 1.194683 at 100iterations 4.0379226E-02 0.6551552 at 110iterations 2.2904173E-02 0.3883407 at 120iterations 1.2999508E-02 0.2173939 at 130iterations 7.3944563E-03 0.1270518 at 140iterations 4.2027025E-03 7.4083328E-02 at 150iterations 2.4022339E-03 4.1885376E-02 at 160iterations 1.3776785E-03 2.3902893E-02 at 170iterations 7.9814246E-04 1.5617371E-02 at 180iterations finished qdiffx linear iterations at : 11:33:23 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 7.9814246E-04 1.5617371E-02 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 11:33:23 15.472u 0.291s 0:16.09 97.9% 0+0k 0+0io 0pf+0w