Wed Dec 28 11:02:09 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 11:02:10 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: 264 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6284978 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): -5.893000 34.79600 ymin,ymax (A): -3.645000 48.44100 zmin,zma (A): -24.47800 32.16500 x,y,z range (A): 40.68900 52.08600 56.64300 scale (grids/A): 0.6284978 object centre (A): 14.45150 22.39800 3.843501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.5999 centred at (gu) : 90.84846 92.56151 89.94590 assigned negative charge : -290.6002 centred at (gu) : 90.96577 92.71867 89.87730 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5437 nv = 96 ne = 84 npr = 39766 no. pairs analyzed = 39766 no. exposed pairs = 2506 no. arc points = 17435 no. surface atoms = 850 nbur = 1120 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 3060 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1767 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9348572E-09 6.6383476E-09 midg,1,midg; midg,igrid,midg 6.9815154E-09 -1.3697589E-08 1,midg,midg; igrid,midg,midg 8.0757951E-09 -6.1115220E-09 gauss-seidel spectral radius is 0.9868343 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 11:02:11 rms-change max change #iterations 0.1174928 21.45269 at 10iterations 1.1135276E-02 1.651908 at 20iterations 1.0571702E-03 0.1757689 at 30iterations 9.9295918E-05 1.4598846E-02 at 40iterations 9.5568448E-06 1.7306805E-03 at 50iterations finished qdiffx linear iterations at : 11:02:16 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 9.5568448E-06 1.7306805E-03 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.340000 DelPhi exited at 11:02:18 5.348u 0.405s 0:08.49 67.6% 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 11:02:19 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: 264 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: 1.885493 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): -5.893000 34.79600 ymin,ymax (A): -3.645000 48.44100 zmin,zma (A): -24.47800 32.16500 x,y,z range (A): 40.68900 52.08600 56.64300 scale (grids/A): 1.885493 object centre (A): 14.45150 22.39800 3.843501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.5999 centred at (gu) : 92.54536 97.68456 89.83736 assigned negative charge : -290.6002 centred at (gu) : 92.89746 98.15613 89.63196 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 57857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17435 grid for indexing accessible points = 1.400000 m= 22166 mr = 40040 m= 3407 mr = 16912 m= 162 mr = 2228 m= 4 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 2913 time to turn everything in is 0.5000000 number of dielectric boundary points 24340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14462 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) : 0.6284978 object centre at (A) : 14.45150 22.39800 3.843501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1339178E-02 1.9588653E-02 midg,1,midg; midg,igrid,midg 2.6167732E-02 -1.4414126E-02 1,midg,midg; igrid,midg,midg 6.8054702E-03 -6.7984872E-03 gauss-seidel spectral radius is 0.9985309 estimated iterations to convergence 207 setup time was (sec) 0.8800000 now iterating at: 11:02:20 rms-change max change #iterations 3.565315 176.5744 at 10iterations 1.614341 60.75956 at 20iterations 0.7375101 25.65430 at 30iterations 0.3355602 12.18091 at 40iterations 0.1529172 5.498508 at 50iterations 6.9690593E-02 2.514618 at 60iterations 3.1672303E-02 1.211643 at 70iterations 1.4376450E-02 0.5775332 at 80iterations 6.5301592E-03 0.2321799 at 90iterations 2.9809168E-03 0.1053925 at 100iterations 1.3561326E-03 4.6727180E-02 at 110iterations 6.1811617E-04 2.3807049E-02 at 120iterations finished qdiffx linear iterations at : 11:02:33 total time elapsed so far: 13.16000 # loops : 120 mean,max change (kT/e) : 6.1811617E-04 2.3807049E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.34000 DelPhi exited at 11:02:34 13.340u 0.640s 0:15.50 90.1% 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 Wed Dec 28 2011 at 11:02:34 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: 264 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.828240 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): -5.893000 34.79600 ymin,ymax (A): -3.645000 48.44100 zmin,zma (A): -24.47800 32.16500 x,y,z range (A): 40.68900 52.08600 56.64300 scale (grids/A): 2.828240 object centre (A): 14.45150 22.39800 3.843501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 2.000006 assigned positive charge : 292.5999 centred at (gu) : 93.81804 101.5268 89.75593 assigned negative charge : -290.6002 centred at (gu) : 94.34617 102.2341 89.44804 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 133597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17435 grid for indexing accessible points = 1.400000 m= 70267 mr = 96502 m= 26705 mr = 58572 m= 6157 mr = 22332 m= 765 mr = 4758 m= 65 mr = 533 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 9410 time to turn everything in is 1.260000 number of dielectric boundary points 54812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 14704 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) : 1.885493 object centre at (A) : 14.45150 22.39800 3.843501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9743405 7.4012786E-02 midg,1,midg; midg,igrid,midg 0.2806374 -0.1717397 1,midg,midg; igrid,midg,midg 4.5503177E-02 -5.4607242E-02 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 1.580000 now iterating at: 11:02:36 rms-change max change #iterations 8.410715 388.5197 at 10iterations 4.816014 151.1079 at 20iterations 2.736295 106.3814 at 30iterations 1.557148 44.63961 at 40iterations 0.8826255 22.27183 at 50iterations 0.4989539 12.02309 at 60iterations 0.2825533 6.615664 at 70iterations 0.1599619 3.778885 at 80iterations 9.0323694E-02 1.939728 at 90iterations 5.1111918E-02 1.099812 at 100iterations 2.8781742E-02 0.5718002 at 110iterations 1.6263993E-02 0.4207649 at 120iterations 9.1738366E-03 0.1817427 at 130iterations 5.1823803E-03 0.1076484 at 140iterations 2.9266276E-03 5.9324265E-02 at 150iterations 1.6527132E-03 3.4761712E-02 at 160iterations 9.3212840E-04 2.0044327E-02 at 170iterations 5.2508787E-04 1.0226250E-02 at 180iterations finished qdiffx linear iterations at : 11:02:52 total time elapsed so far: 17.70000 # loops : 180 mean,max change (kT/e) : 5.2508787E-04 1.0226250E-02 energy calculations done at 17.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.87000 DelPhi exited at 11:02:53 17.870u 0.468s 0:18.63 98.3% 0+0k 0+0io 0pf+0w