Wed Dec 28 11:03:52 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 28 2011 at 11:03:52 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.5461211 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): -34.85200 12.02700 ymin,ymax (A): 0.1760000 42.72800 zmin,zma (A): -4.488000 60.69900 x,y,z range (A): 46.87900 42.55200 65.18700 scale (grids/A): 0.5461211 object centre (A): -11.41250 21.45200 28.10550 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 293.7999 centred at (gu) : 89.82669 89.38232 89.88717 assigned negative charge : -291.8002 centred at (gu) : 89.73858 89.51649 89.87932 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 3880 nv = 96 ne = 84 npr = 39669 no. pairs analyzed = 39669 no. exposed pairs = 2545 no. arc points = 17922 no. surface atoms = 859 nbur = 1111 mkacc time = 0.1100000 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 = 1.568000 m= 143 mr = 1999 m= 0 mr = 10 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1814 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 5005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0473601E-11 1.5276568E-10 midg,1,midg; midg,igrid,midg 8.1888329E-10 -4.0701262E-10 1,midg,midg; igrid,midg,midg -2.8062436E-10 4.8365101E-10 gauss-seidel spectral radius is 0.9826350 estimated iterations to convergence 63 setup time was (sec) 0.7300000 now iterating at: 11:03:54 rms-change max change #iterations 6.0604520E-02 11.60414 at 10iterations 3.9724093E-03 0.7289486 at 20iterations 2.6552906E-04 5.4870188E-02 at 30iterations 1.7891649E-05 3.7589073E-03 at 40iterations 1.1903190E-06 2.5558472E-04 at 50iterations finished qdiffx linear iterations at : 11:03:59 total time elapsed so far: 6.310000 # loops : 50 mean,max change (kT/e) : 1.1903190E-06 2.5558472E-04 energy calculations done at 6.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.480000 DelPhi exited at 11:04:00 6.480u 0.732s 0:08.10 89.0% 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 28 2011 at 11:04:00 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.638363 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): -34.85200 12.02700 ymin,ymax (A): 0.1760000 42.72800 zmin,zma (A): -4.488000 60.69900 x,y,z range (A): 46.87900 42.55200 65.18700 scale (grids/A): 1.638363 object centre (A): -11.41250 21.45200 28.10550 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 293.7999 centred at (gu) : 89.48015 88.14684 89.66138 assigned negative charge : -291.8002 centred at (gu) : 89.21606 88.54973 89.63780 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 42498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 13190 mr = 28251 m= 1333 mr = 9450 m= 39 mr = 702 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 952 time to turn everything in is 0.4500000 number of dielectric boundary points 18655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 250 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 14151 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) : 0.5461211 object centre at (A) : -11.41250 21.45200 28.10550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6752474E-02 1.6633999E-02 midg,1,midg; midg,igrid,midg 1.5321043E-03 -4.8028510E-03 1,midg,midg; igrid,midg,midg -2.6261457E-03 -7.6923077E-04 gauss-seidel spectral radius is 0.9980758 estimated iterations to convergence 181 setup time was (sec) 0.9600000 now iterating at: 11:04:02 rms-change max change #iterations 2.684131 136.8392 at 10iterations 1.092265 49.18433 at 20iterations 0.4438938 21.99351 at 30iterations 0.1799942 9.029305 at 40iterations 7.2985284E-02 3.035019 at 50iterations 2.9570343E-02 1.308524 at 60iterations 1.1996564E-02 0.5015965 at 70iterations 4.8795459E-03 0.2278628 at 80iterations 1.9760649E-03 8.1735611E-02 at 90iterations 8.0320012E-04 3.5882473E-02 at 100iterations 3.2736437E-04 1.3931274E-02 at 110iterations 1.3270939E-04 5.6724548E-03 at 120iterations finished qdiffx linear iterations at : 11:04:20 total time elapsed so far: 18.48000 # loops : 120 mean,max change (kT/e) : 1.3270939E-04 5.6724548E-03 energy calculations done at 18.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.73000 DelPhi exited at 11:04:20 18.739u 0.822s 0:19.94 98.0% 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 28 2011 at 11:04:20 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.457545 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): -34.85200 12.02700 ymin,ymax (A): 0.1760000 42.72800 zmin,zma (A): -4.488000 60.69900 x,y,z range (A): 46.87900 42.55200 65.18700 scale (grids/A): 2.457545 object centre (A): -11.41250 21.45200 28.10550 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 293.7999 centred at (gu) : 89.22020 87.22025 89.49210 assigned negative charge : -291.8002 centred at (gu) : 88.82405 87.82456 89.45685 start vw surface at 0.1100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 98396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17922 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 45494 mr = 68727 m= 13063 mr = 36633 m= 2197 mr = 10243 m= 165 mr = 1514 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 3167 time to turn everything in is 1.040000 number of dielectric boundary points 42128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 14685 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) : 1.638363 object centre at (A) : -11.41250 21.45200 28.10550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2182912 0.1950260 midg,1,midg; midg,igrid,midg -2.1093988E-03 -7.5237714E-02 1,midg,midg; igrid,midg,midg -5.0378215E-02 -2.2086533E-02 gauss-seidel spectral radius is 0.9990659 estimated iterations to convergence 259 setup time was (sec) 1.630000 now iterating at: 11:04:23 rms-change max change #iterations 6.843717 325.2789 at 10iterations 3.700020 163.2144 at 20iterations 1.998849 54.54170 at 30iterations 1.072424 31.16293 at 40iterations 0.5756626 15.41791 at 50iterations 0.3082780 7.970079 at 60iterations 0.1651289 4.141855 at 70iterations 8.8226669E-02 2.214410 at 80iterations 4.7187373E-02 1.332104 at 90iterations 2.5284847E-02 0.6213226 at 100iterations 1.3536437E-02 0.3861618 at 110iterations 7.2259046E-03 0.1868021 at 120iterations 3.8615547E-03 9.8106384E-02 at 130iterations 2.0715469E-03 5.3618908E-02 at 140iterations 1.1023920E-03 2.7501583E-02 at 150iterations 5.9119699E-04 1.4385223E-02 at 160iterations 3.1571180E-04 8.8710785E-03 at 170iterations 1.6920893E-04 4.1475296E-03 at 180iterations finished qdiffx linear iterations at : 11:04:47 total time elapsed so far: 25.71000 # loops : 180 mean,max change (kT/e) : 1.6920893E-04 4.1475296E-03 energy calculations done at 25.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 25.88000 DelPhi exited at 11:04:48 25.888u 0.862s 0:27.16 98.4% 0+0k 0+0io 0pf+0w