Mon Oct 10 14:01:52 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 Mon Oct 10 2011 at 14:01:52 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 = 3735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5927307 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): -5.844000 47.37700 ymin,ymax (A): 12.48100 72.54200 zmin,zma (A): -28.13200 25.74800 x,y,z range (A): 53.22100 60.06100 53.88000 scale (grids/A): 0.5927307 object centre (A): 20.76650 42.51150 -1.192000 number of atom coordinates read : 3735 total number of charged atoms : 3611 net assigned charge : 11.00003 assigned positive charge : 562.1834 centred at (gu) : 88.73232 90.95304 89.81666 assigned negative charge : -551.1855 centred at (gu) : 88.77927 90.81418 89.67030 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8420 nv = 96 ne = 84 npr = 78824 no. pairs analyzed = 78824 no. exposed pairs = 4027 no. arc points = 27096 no. surface atoms = 1375 nbur = 2360 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 = 1.456000 m= 343 mr = 5021 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3900000 number of dielectric boundary points 3704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2843 ## 302 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10886 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6162907E-09 9.1635588E-09 midg,1,midg; midg,igrid,midg -1.7121209E-09 1.1530759E-08 1,midg,midg; igrid,midg,midg 7.4142958E-09 1.2989666E-09 gauss-seidel spectral radius is 0.9853480 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 14:01:53 rms-change max change #iterations 0.1279801 16.49160 at 10iterations 1.2466548E-02 1.674213 at 20iterations 2.1245151E-03 0.3184967 at 30iterations 6.5683416E-04 9.6233368E-02 at 40iterations 2.3259292E-04 3.3248901E-02 at 50iterations finished qdiffx linear iterations at : 14:01:56 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 2.3259292E-04 3.3248901E-02 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 14:01:57 3.183u 0.143s 0:04.27 77.7% 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 14:01:57 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 = 3735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.778192 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): -5.844000 47.37700 ymin,ymax (A): 12.48100 72.54200 zmin,zma (A): -28.13200 25.74800 x,y,z range (A): 53.22100 60.06100 53.88000 scale (grids/A): 1.778192 object centre (A): 20.76650 42.51150 -1.192000 number of atom coordinates read : 3735 total number of charged atoms : 3611 net assigned charge : 11.00003 assigned positive charge : 562.1834 centred at (gu) : 86.19587 92.85801 89.44869 assigned negative charge : -551.1855 centred at (gu) : 86.33749 92.44214 89.01014 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 92179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27096 grid for indexing accessible points = 1.400000 m= 32417 mr = 67725 m= 4330 mr = 24612 m= 178 mr = 2726 m= 0 mr = 36 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1742 time to turn everything in is 0.6000000 number of dielectric boundary points 34005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 28192 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) : 0.5927307 object centre at (A) : 20.76650 42.51150 -1.192000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3945160E-02 3.2490704E-02 midg,1,midg; midg,igrid,midg 1.2139113E-02 6.0290508E-02 1,midg,midg; igrid,midg,midg 2.6531154E-02 2.3165189E-02 gauss-seidel spectral radius is 0.9985255 estimated iterations to convergence 207 setup time was (sec) 0.8600000 now iterating at: 14:01:58 rms-change max change #iterations 4.499979 171.9832 at 10iterations 2.050927 63.12026 at 20iterations 0.9380926 27.97626 at 30iterations 0.4272245 11.90566 at 40iterations 0.1946688 6.160397 at 50iterations 8.9284621E-02 2.661154 at 60iterations 4.0920109E-02 1.210169 at 70iterations 1.8937647E-02 0.5326843 at 80iterations 8.8338451E-03 0.2674789 at 90iterations 4.2835134E-03 0.1307831 at 100iterations 2.1911093E-03 6.7943573E-02 at 110iterations 1.2192029E-03 3.9455414E-02 at 120iterations finished qdiffx linear iterations at : 14:02:04 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 1.2192029E-03 3.9455414E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 14:02:05 7.568u 0.213s 0:08.77 88.5% 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 Mon Oct 10 2011 at 14:02:06 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 = 3735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.667288 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): -5.844000 47.37700 ymin,ymax (A): 12.48100 72.54200 zmin,zma (A): -28.13200 25.74800 x,y,z range (A): 53.22100 60.06100 53.88000 scale (grids/A): 2.667288 object centre (A): 20.76650 42.51150 -1.192000 number of atom coordinates read : 3735 total number of charged atoms : 3611 net assigned charge : 11.00003 assigned positive charge : 562.1834 centred at (gu) : 84.29356 94.28664 89.17257 assigned negative charge : -551.1855 centred at (gu) : 84.50615 93.66316 88.51508 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 214227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27096 grid for indexing accessible points = 1.400000 m= 108301 mr = 164168 m= 36006 mr = 90399 m= 7501 mr = 29326 m= 796 mr = 5791 m= 14 mr = 513 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 5837 time to turn everything in is 1.560000 number of dielectric boundary points 76646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 28877 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) : 1.778192 object centre at (A) : 20.76650 42.51150 -1.192000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1805422 0.3182618 midg,1,midg; midg,igrid,midg 0.3610722 0.6066418 1,midg,midg; igrid,midg,midg 0.3092103 0.3464237 gauss-seidel spectral radius is 0.9992387 estimated iterations to convergence 286 setup time was (sec) 1.860000 now iterating at: 14:02:08 rms-change max change #iterations 10.83357 248.3582 at 10iterations 6.282229 169.2480 at 20iterations 3.619752 80.54518 at 30iterations 2.084390 40.93189 at 40iterations 1.197474 20.76046 at 50iterations 0.6872320 12.00266 at 60iterations 0.3936548 7.912689 at 70iterations 0.2255431 3.769116 at 80iterations 0.1292316 2.204459 at 90iterations 7.4068636E-02 1.392279 at 100iterations 4.2431906E-02 0.8036313 at 110iterations 2.4482593E-02 0.4230881 at 120iterations 1.4206329E-02 0.2633133 at 130iterations 8.3680293E-03 0.1362305 at 140iterations 5.0511393E-03 8.5853577E-02 at 150iterations 3.1771383E-03 5.5328369E-02 at 160iterations 2.1084049E-03 3.5499573E-02 at 170iterations 1.4807601E-03 2.5344849E-02 at 180iterations finished qdiffx linear iterations at : 14:02:17 total time elapsed so far: 11.31000 # loops : 180 mean,max change (kT/e) : 1.4807601E-03 2.5344849E-02 energy calculations done at 11.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.48000 DelPhi exited at 14:02:18 11.485u 0.177s 0:11.96 97.4% 0+0k 0+0io 0pf+0w