Sun Oct 9 10:43:24 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 Sun Oct 9 2011 at 10:43:24 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2184 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 0.6303228 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): -1.902000 51.55300 ymin,ymax (A): -25.26700 31.21200 zmin,zma (A): -3.896000 48.36800 x,y,z range (A): 53.45500 56.47900 52.26400 scale (grids/A): 0.6303228 object centre (A): 24.82550 2.972500 22.23600 number of atom coordinates read : 2184 total number of charged atoms : 2047 net assigned charge : 0.5140151 assigned positive charge : 317.9786 centred at (gu) : 89.75845 90.27938 90.48569 assigned negative charge : -317.4653 centred at (gu) : 89.71342 90.15314 90.42653 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5966 nv = 96 ne = 84 npr = 43181 no. pairs analyzed = 43181 no. exposed pairs = 3020 no. arc points = 21188 no. surface atoms = 1009 nbur = 1175 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 3034 m= 0 mr = 35 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3201 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2077 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7058 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4297503E-09 5.3674492E-09 midg,1,midg; midg,igrid,midg -8.2914209E-09 1.0234214E-08 1,midg,midg; igrid,midg,midg -2.9303986E-09 3.6048846E-09 gauss-seidel spectral radius is 0.9869366 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 10:43:24 rms-change max change #iterations 0.1228468 20.43132 at 10iterations 1.1523331E-02 2.037670 at 20iterations 1.0861952E-03 0.1630325 at 30iterations 1.0367285E-04 1.6000748E-02 at 40iterations 1.0114857E-05 1.7547607E-03 at 50iterations finished qdiffx linear iterations at : 10:43:27 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.0114857E-05 1.7547607E-03 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 10:43:28 3.577u 0.184s 0:04.07 92.1% 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 Sun Oct 9 2011 at 10:43:28 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2184 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.890968 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): -1.902000 51.55300 ymin,ymax (A): -25.26700 31.21200 zmin,zma (A): -3.896000 48.36800 x,y,z range (A): 53.45500 56.47900 52.26400 scale (grids/A): 1.890968 object centre (A): 24.82550 2.972500 22.23600 number of atom coordinates read : 2184 total number of charged atoms : 2047 net assigned charge : 0.5140151 assigned positive charge : 317.9786 centred at (gu) : 89.27525 90.83763 91.45670 assigned negative charge : -317.4653 centred at (gu) : 89.14053 90.45974 91.27984 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 64131 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21188 grid for indexing accessible points = 1.400000 m= 21081 mr = 42306 m= 3174 mr = 14622 m= 192 mr = 1964 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 494 time to turn everything in is 0.3200000 number of dielectric boundary points 29614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 16108 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) : 0.6303228 object centre at (A) : 24.82550 2.972500 22.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4248728E-02 3.0741293E-02 midg,1,midg; midg,igrid,midg -1.3452733E-02 2.4043584E-02 1,midg,midg; igrid,midg,midg -2.1202922E-02 4.7909333E-03 gauss-seidel spectral radius is 0.9985862 estimated iterations to convergence 211 setup time was (sec) 0.5600000 now iterating at: 10:43:29 rms-change max change #iterations 3.721966 180.4811 at 10iterations 1.707374 70.13052 at 20iterations 0.7895769 27.56681 at 30iterations 0.3649018 13.06061 at 40iterations 0.1684547 6.044170 at 50iterations 7.7540748E-02 2.885736 at 60iterations 3.5743196E-02 1.176617 at 70iterations 1.6499320E-02 0.5154724 at 80iterations 7.6258732E-03 0.2574196 at 90iterations 3.5252464E-03 0.1250505 at 100iterations 1.6257897E-03 5.6175232E-02 at 110iterations 7.5277872E-04 2.5115192E-02 at 120iterations finished qdiffx linear iterations at : 10:43:36 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 7.5277872E-04 2.5115192E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 10:43:37 8.079u 0.230s 0:08.75 94.8% 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 10:43:37 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2184 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 2.836452 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): -1.902000 51.55300 ymin,ymax (A): -25.26700 31.21200 zmin,zma (A): -3.896000 48.36800 x,y,z range (A): 53.45500 56.47900 52.26400 scale (grids/A): 2.836452 object centre (A): 24.82550 2.972500 22.23600 number of atom coordinates read : 2184 total number of charged atoms : 2047 net assigned charge : 0.5140151 assigned positive charge : 317.9786 centred at (gu) : 88.91285 91.25651 92.18507 assigned negative charge : -317.4653 centred at (gu) : 88.71086 90.68960 91.91978 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 148599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21188 grid for indexing accessible points = 1.400000 m= 69135 mr = 103521 m= 23439 mr = 54502 m= 5539 mr = 18145 m= 848 mr = 4159 m= 56 mr = 575 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1645 time to turn everything in is 0.8400000 number of dielectric boundary points 66693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 16373 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) : 1.890968 object centre at (A) : 24.82550 2.972500 22.23600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1904999 0.3370548 midg,1,midg; midg,igrid,midg -0.1304357 0.2237089 1,midg,midg; igrid,midg,midg -0.2914357 4.7315382E-03 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 1.100000 now iterating at: 10:43:38 rms-change max change #iterations 8.806401 462.9960 at 10iterations 5.087443 110.6753 at 20iterations 2.916979 70.46347 at 30iterations 1.675514 33.36636 at 40iterations 0.9570515 20.12405 at 50iterations 0.5486966 10.74861 at 60iterations 0.3129807 6.156553 at 70iterations 0.1790885 3.497953 at 80iterations 0.1023379 2.012346 at 90iterations 5.8338314E-02 1.130135 at 100iterations 3.3231985E-02 0.6531792 at 110iterations 1.9014146E-02 0.3667316 at 120iterations 1.0853387E-02 0.2062507 at 130iterations 6.1804680E-03 0.1087046 at 140iterations 3.5323775E-03 6.8550110E-02 at 150iterations 2.0163066E-03 3.9558411E-02 at 160iterations 1.1494078E-03 2.3770213E-02 at 170iterations 6.5784721E-04 1.2511253E-02 at 180iterations finished qdiffx linear iterations at : 10:43:50 total time elapsed so far: 13.27000 # loops : 180 mean,max change (kT/e) : 6.5784721E-04 1.2511253E-02 energy calculations done at 13.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 10:43:51 13.396u 0.276s 0:13.97 97.7% 0+0k 0+0io 0pf+0w