Sun Oct 9 13:36:42 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 Sun Oct 9 2011 at 13:36:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2359 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: 0.7087398 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): -0.4970000 45.46000 ymin,ymax (A): 36.37400 86.60400 zmin,zma (A): -22.33500 24.71500 x,y,z range (A): 45.95700 50.23000 47.05000 scale (grids/A): 0.7087398 object centre (A): 22.48150 61.48900 1.190001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.89289 89.81612 91.03377 assigned negative charge : -356.3476 centred at (gu) : 89.99497 90.03686 90.95425 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7987 nv = 96 ne = 84 npr = 48324 no. pairs analyzed = 48324 no. exposed pairs = 2956 no. arc points = 20370 no. surface atoms = 998 nbur = 1361 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4475 m= 5 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1923 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7727527E-08 7.1440454E-08 midg,1,midg; midg,igrid,midg 1.4298526E-07 -1.1445390E-07 1,midg,midg; igrid,midg,midg 7.2613567E-08 -4.6530158E-08 gauss-seidel spectral radius is 0.9896508 estimated iterations to convergence 80 setup time was (sec) 0.4800000 now iterating at: 13:36:43 rms-change max change #iterations 0.2141908 31.75369 at 10iterations 2.7085623E-02 4.657257 at 20iterations 3.6747230E-03 0.4620066 at 30iterations 6.8416039E-04 9.5737457E-02 at 40iterations 1.9082426E-04 2.9926300E-02 at 50iterations finished qdiffx linear iterations at : 13:36:45 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.9082426E-04 2.9926300E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 13:36:46 3.072u 0.140s 0:03.47 92.5% 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 Sun Oct 9 2011 at 13:36:46 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 = 2359 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: 2.126220 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): -0.4970000 45.46000 ymin,ymax (A): 36.37400 86.60400 zmin,zma (A): -22.33500 24.71500 x,y,z range (A): 45.95700 50.23000 47.05000 scale (grids/A): 2.126220 object centre (A): 22.48150 61.48900 1.190001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.67831 89.44800 93.10097 assigned negative charge : -356.3476 centred at (gu) : 89.98463 90.11034 92.86244 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84790 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20370 grid for indexing accessible points = 1.400000 m= 32787 mr = 59414 m= 6036 mr = 24439 m= 587 mr = 3882 m= 17 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 36184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17589 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) : 0.7087398 object centre at (A) : 22.48150 61.48900 1.190001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8465716E-03 2.1586545E-02 midg,1,midg; midg,igrid,midg 0.1003576 -7.4690484E-02 1,midg,midg; igrid,midg,midg 7.3085185E-03 -9.3598291E-03 gauss-seidel spectral radius is 0.9988680 estimated iterations to convergence 235 setup time was (sec) 0.8400000 now iterating at: 13:36:47 rms-change max change #iterations 4.981460 211.9686 at 10iterations 2.489898 84.32704 at 20iterations 1.240488 37.03938 at 30iterations 0.6235443 18.64157 at 40iterations 0.3125678 10.20397 at 50iterations 0.1570342 4.445189 at 60iterations 7.8928865E-02 2.515840 at 70iterations 3.9511077E-02 1.074497 at 80iterations 1.9926948E-02 0.5612717 at 90iterations 1.0109451E-02 0.2909765 at 100iterations 5.1595764E-03 0.1632156 at 110iterations 2.6804784E-03 8.0965996E-02 at 120iterations finished qdiffx linear iterations at : 13:36:53 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 2.6804784E-03 8.0965996E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 13:36:53 6.919u 0.164s 0:07.41 95.4% 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 Sun Oct 9 2011 at 13:36:53 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 = 2359 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: 3.189329 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): -0.4970000 45.46000 ymin,ymax (A): 36.37400 86.60400 zmin,zma (A): -22.33500 24.71500 x,y,z range (A): 45.95700 50.23000 47.05000 scale (grids/A): 3.189329 object centre (A): 22.48150 61.48900 1.190001 number of atom coordinates read : 2359 total number of charged atoms : 2217 net assigned charge : 1.500017 assigned positive charge : 357.8471 centred at (gu) : 89.51743 89.17171 94.65136 assigned negative charge : -356.3476 centred at (gu) : 89.97692 90.16540 94.29359 start vw surface at 0.1300000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 195478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20370 grid for indexing accessible points = 1.400000 m= 103309 mr = 143378 m= 40614 mr = 84984 m= 11414 mr = 32981 m= 2289 mr = 8616 m= 262 mr = 1714 m= 17 mr = 143 m= 0 mr = 6 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.870000 number of dielectric boundary points 81561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 17736 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) : 2.126220 object centre at (A) : 22.48150 61.48900 1.190001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7854776E-03 0.3533467 midg,1,midg; midg,igrid,midg 1.662564 -0.8155193 1,midg,midg; igrid,midg,midg 2.9206507E-02 -4.4304796E-02 gauss-seidel spectral radius is 0.9993091 estimated iterations to convergence 300 setup time was (sec) 2.150000 now iterating at: 13:36:56 rms-change max change #iterations 11.16328 375.1423 at 10iterations 6.678666 134.2786 at 20iterations 3.985163 80.08447 at 30iterations 2.373313 47.53814 at 40iterations 1.406837 31.13556 at 50iterations 0.8323563 14.59468 at 60iterations 0.4909269 8.562844 at 70iterations 0.2903863 5.787205 at 80iterations 0.1711462 2.821857 at 90iterations 0.1009797 1.670746 at 100iterations 5.9367578E-02 1.025757 at 110iterations 3.5093334E-02 0.6144485 at 120iterations 2.0815752E-02 0.3913599 at 130iterations 1.2473293E-02 0.2132931 at 140iterations 7.5921784E-03 0.1547890 at 150iterations 4.7536679E-03 8.7484360E-02 at 160iterations 3.1126018E-03 6.8204880E-02 at 170iterations 2.1589822E-03 4.6669006E-02 at 180iterations finished qdiffx linear iterations at : 13:37:06 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 2.1589822E-03 4.6669006E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 13:37:07 13.141u 0.174s 0:13.58 98.0% 0+0k 0+0io 0pf+0w