Wed Dec 21 14:21:11 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+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 Wed Dec 21 2011 at 14:21:12 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: 244 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: 0.6284978 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 : 289.4000 centred at (gu) : 90.85567 92.57782 89.94059 assigned negative charge : -287.4003 centred at (gu) : 90.97707 92.73354 89.87265 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 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 = 0.1100000 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 = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 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 0.4100000 number of grid points assigned charge 6372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8475625E-09 6.5417121E-09 midg,1,midg; midg,igrid,midg 6.8454162E-09 -1.3386494E-08 1,midg,midg; igrid,midg,midg 8.2003986E-09 -6.3402350E-09 gauss-seidel spectral radius is 0.9868343 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 14:21:12 rms-change max change #iterations 0.1145234 20.79835 at 10iterations 1.0845817E-02 1.559143 at 20iterations 1.0328077E-03 0.1756740 at 30iterations 9.6924741E-05 1.5113831E-02 at 40iterations 9.3216522E-06 1.7447472E-03 at 50iterations finished qdiffx linear iterations at : 14:21:16 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 9.3216522E-06 1.7447472E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 14:21:19 4.329u 0.264s 0:07.79 58.7% 0+0k 0+0io 6pf+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 21 2011 at 14:21:21 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: 244 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 : 289.4000 centred at (gu) : 92.56700 97.73351 89.82148 assigned negative charge : -287.4003 centred at (gu) : 92.93145 98.20081 89.61810 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 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 = 0.2600000 no. cavity mid-points inaccessible to solvent = 2913 time to turn everything in is 0.5500000 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 0.7000000 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 4.1378777E-02 1.9466704E-02 midg,1,midg; midg,igrid,midg 2.5882633E-02 -1.3802736E-02 1,midg,midg; igrid,midg,midg 6.7991894E-03 -6.9958987E-03 gauss-seidel spectral radius is 0.9985309 estimated iterations to convergence 207 setup time was (sec) 0.8800000 now iterating at: 14:21:23 rms-change max change #iterations 3.509394 176.5744 at 10iterations 1.590096 60.75900 at 20iterations 0.7262351 25.86191 at 30iterations 0.3304583 12.43616 at 40iterations 0.1505034 5.203205 at 50iterations 6.8627656E-02 2.537048 at 60iterations 3.1192152E-02 1.205383 at 70iterations 1.4156905E-02 0.5952921 at 80iterations 6.4321826E-03 0.2221851 at 90iterations 2.9349951E-03 0.1046677 at 100iterations 1.3348670E-03 4.7134399E-02 at 110iterations 6.0846511E-04 2.3177028E-02 at 120iterations finished qdiffx linear iterations at : 14:21:34 total time elapsed so far: 11.69000 # loops : 120 mean,max change (kT/e) : 6.0846511E-04 2.3177028E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 14:21:40 11.883u 0.324s 0:18.75 65.0% 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 21 2011 at 14:21:41 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: 244 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: 2.828240 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 : 289.4000 centred at (gu) : 93.85051 101.6002 89.73214 assigned negative charge : -287.4003 centred at (gu) : 94.39715 102.3012 89.42725 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 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 = 0.8000000 no. cavity mid-points inaccessible to solvent = 9410 time to turn everything in is 1.370000 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 1.510000 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 0.9749999 7.3117383E-02 midg,1,midg; midg,igrid,midg 0.2770734 -0.1649877 1,midg,midg; igrid,midg,midg 4.3924443E-02 -5.5756055E-02 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 1.690000 now iterating at: 14:21:43 rms-change max change #iterations 8.287159 388.5198 at 10iterations 4.749777 150.8363 at 20iterations 2.698914 106.2873 at 30iterations 1.535980 44.09110 at 40iterations 0.8709608 21.95549 at 50iterations 0.4923321 12.10966 at 60iterations 0.2788178 6.638863 at 70iterations 0.1578298 3.806368 at 80iterations 8.9135163E-02 1.851086 at 90iterations 5.0458107E-02 1.118184 at 100iterations 2.8412020E-02 0.5497837 at 110iterations 1.6059857E-02 0.4181309 at 120iterations 9.0565681E-03 0.1787761 at 130iterations 5.1181759E-03 0.1098132 at 140iterations 2.8906914E-03 5.7186127E-02 at 150iterations 1.6322160E-03 3.4726933E-02 at 160iterations 9.2052243E-04 2.0227432E-02 at 170iterations 5.1855057E-04 1.0462523E-02 at 180iterations finished qdiffx linear iterations at : 14:22:01 total time elapsed so far: 19.73000 # loops : 180 mean,max change (kT/e) : 5.1855057E-04 1.0462523E-02 energy calculations done at 19.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.92000 DelPhi exited at 14:22:12 19.925u 0.309s 0:31.56 64.0% 0+0k 0+0io 0pf+0w