Tue Oct 11 06:12:14 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 Tue Oct 11 2011 at 06:12:14 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2030 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7312164 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): 20.18500 64.35300 ymin,ymax (A): -3.419000 34.97000 zmin,zma (A): 22.96600 71.65200 x,y,z range (A): 44.16800 38.38900 48.68600 scale (grids/A): 0.7312164 object centre (A): 42.26900 15.77550 47.30900 number of atom coordinates read : 2030 total number of charged atoms : 1900 net assigned charge : 4.500006 assigned positive charge : 306.8701 centred at (gu) : 89.88229 89.07104 88.52162 assigned negative charge : -302.3702 centred at (gu) : 90.03878 89.18262 88.50913 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7470 nv = 96 ne = 84 npr = 40777 no. pairs analyzed = 40777 no. exposed pairs = 2486 no. arc points = 16980 no. surface atoms = 848 nbur = 1182 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 4384 m= 7 mr = 125 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 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1420 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1253460E-08 5.6887249E-08 midg,1,midg; midg,igrid,midg 1.8208351E-07 -2.0777220E-08 1,midg,midg; igrid,midg,midg 1.9181429E-07 -6.0898728E-08 gauss-seidel spectral radius is 0.9902416 estimated iterations to convergence 82 setup time was (sec) 0.6300000 now iterating at: 06:12:15 rms-change max change #iterations 0.2337911 28.80099 at 10iterations 3.1280443E-02 4.596313 at 20iterations 4.2214026E-03 0.6075211 at 30iterations 6.8540493E-04 7.8308105E-02 at 40iterations 1.5612289E-04 1.8441200E-02 at 50iterations finished qdiffx linear iterations at : 06:12:18 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.5612289E-04 1.8441200E-02 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 06:12:19 4.245u 0.253s 0:04.80 93.5% 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 Tue Oct 11 2011 at 06:12:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2030 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: 2.193649 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): 20.18500 64.35300 ymin,ymax (A): -3.419000 34.97000 zmin,zma (A): 22.96600 71.65200 x,y,z range (A): 44.16800 38.38900 48.68600 scale (grids/A): 2.193649 object centre (A): 42.26900 15.77550 47.30900 number of atom coordinates read : 2030 total number of charged atoms : 1900 net assigned charge : 4.500006 assigned positive charge : 306.8701 centred at (gu) : 89.64697 87.21342 85.56492 assigned negative charge : -302.3702 centred at (gu) : 90.11658 87.54781 85.52759 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16980 grid for indexing accessible points = 1.400000 m= 33654 mr = 56269 m= 7570 mr = 25878 m= 861 mr = 5254 m= 21 mr = 470 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 32936 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15122 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) : 0.7312164 object centre at (A) : 42.26900 15.77550 47.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3971622E-04 2.4829172E-02 midg,1,midg; midg,igrid,midg 3.8640387E-02 -5.2176891E-03 1,midg,midg; igrid,midg,midg 5.2871052E-02 2.5359163E-02 gauss-seidel spectral radius is 0.9988906 estimated iterations to convergence 238 setup time was (sec) 1.030000 now iterating at: 06:12:20 rms-change max change #iterations 4.810451 183.1473 at 10iterations 2.423679 79.63122 at 20iterations 1.228750 38.47985 at 30iterations 0.6229121 18.18159 at 40iterations 0.3150676 8.976018 at 50iterations 0.1592378 4.420214 at 60iterations 8.0857933E-02 2.379128 at 70iterations 4.0973257E-02 1.265938 at 80iterations 2.0748695E-02 0.6331005 at 90iterations 1.0564121E-02 0.3166609 at 100iterations 5.4063965E-03 0.1486168 at 110iterations 2.7981228E-03 8.3591461E-02 at 120iterations finished qdiffx linear iterations at : 06:12:29 total time elapsed so far: 9.500000 # loops : 120 mean,max change (kT/e) : 2.7981228E-03 8.3591461E-02 energy calculations done at 9.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.680000 DelPhi exited at 06:12:29 9.686u 0.260s 0:10.44 95.2% 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 Tue Oct 11 2011 at 06:12:29 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2030 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: 3.290474 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): 20.18500 64.35300 ymin,ymax (A): -3.419000 34.97000 zmin,zma (A): 22.96600 71.65200 x,y,z range (A): 44.16800 38.38900 48.68600 scale (grids/A): 3.290474 object centre (A): 42.26900 15.77550 47.30900 number of atom coordinates read : 2030 total number of charged atoms : 1900 net assigned charge : 4.500006 assigned positive charge : 306.8701 centred at (gu) : 89.47057 85.82011 83.34731 assigned negative charge : -302.3702 centred at (gu) : 90.17488 86.32169 83.29136 start vw surface at 0.1300000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 181097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16980 grid for indexing accessible points = 1.400000 m= 101905 mr = 134936 m= 45216 mr = 85483 m= 14741 mr = 37672 m= 3252 mr = 11676 m= 433 mr = 2374 m= 26 mr = 317 m= 0 mr = 8 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.050000 number of dielectric boundary points 74204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 15192 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) : 2.193649 object centre at (A) : 42.26900 15.77550 47.30900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5145742E-02 -0.1061348 midg,1,midg; midg,igrid,midg 0.2903817 -2.5785055E-02 1,midg,midg; igrid,midg,midg 0.4340532 0.4215259 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 2.430000 now iterating at: 06:12:32 rms-change max change #iterations 10.65317 359.5981 at 10iterations 6.378667 125.1304 at 20iterations 3.823312 74.60440 at 30iterations 2.277213 44.85030 at 40iterations 1.355813 25.70352 at 50iterations 0.8024165 14.31948 at 60iterations 0.4761051 8.210245 at 70iterations 0.2812387 5.231581 at 80iterations 0.1664341 3.082329 at 90iterations 9.8076932E-02 1.752886 at 100iterations 5.8132373E-02 0.9794312 at 110iterations 3.4453996E-02 0.5922546 at 120iterations 2.0518446E-02 0.3478012 at 130iterations 1.2382641E-02 0.2337799 at 140iterations 7.6120812E-03 0.1293812 at 150iterations 4.8319763E-03 8.4568024E-02 at 160iterations 3.2279454E-03 5.4393768E-02 at 170iterations 2.3025814E-03 3.6369324E-02 at 180iterations finished qdiffx linear iterations at : 06:12:46 total time elapsed so far: 16.67000 # loops : 180 mean,max change (kT/e) : 2.3025814E-03 3.6369324E-02 energy calculations done at 16.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.85000 DelPhi exited at 06:12:47 16.848u 0.342s 0:17.46 98.3% 0+0k 0+0io 0pf+0w