Mon Oct 10 18:51:37 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 Mon Oct 10 2011 at 18:51:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 0.6290531 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): 0.6050001 40.41800 ymin,ymax (A): 37.48700 94.08000 zmin,zma (A): 16.11400 70.88300 x,y,z range (A): 39.81300 56.59300 54.76900 scale (grids/A): 0.6290531 object centre (A): 20.51150 65.78350 43.49850 number of atom coordinates read : 2120 total number of charged atoms : 1986 net assigned charge : 2.500004 assigned positive charge : 311.8044 centred at (gu) : 89.69819 87.53400 90.06084 assigned negative charge : -309.3048 centred at (gu) : 89.81154 87.63467 90.07423 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5806 nv = 96 ne = 84 npr = 42337 no. pairs analyzed = 42337 no. exposed pairs = 2727 no. arc points = 19356 no. surface atoms = 919 nbur = 1201 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3189 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3000000 number of dielectric boundary points 2908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1911 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 6928 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2877396E-09 1.5223832E-09 midg,1,midg; midg,igrid,midg 1.5905101E-08 -2.5955578E-09 1,midg,midg; igrid,midg,midg 1.0740354E-08 -5.0525872E-09 gauss-seidel spectral radius is 0.9868735 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 18:51:38 rms-change max change #iterations 0.1213225 22.35863 at 10iterations 1.1416656E-02 1.812447 at 20iterations 1.2089444E-03 0.2101860 at 30iterations 1.7594748E-04 3.1477928E-02 at 40iterations 3.8993567E-05 7.4386597E-03 at 50iterations finished qdiffx linear iterations at : 18:51:41 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 3.8993567E-05 7.4386597E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 18:51:42 4.097u 0.288s 0:04.78 91.4% 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 Mon Oct 10 2011 at 18:51:42 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 = 2120 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: 1.887159 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): 0.6050001 40.41800 ymin,ymax (A): 37.48700 94.08000 zmin,zma (A): 16.11400 70.88300 x,y,z range (A): 39.81300 56.59300 54.76900 scale (grids/A): 1.887159 object centre (A): 20.51150 65.78350 43.49850 number of atom coordinates read : 2120 total number of charged atoms : 1986 net assigned charge : 2.500004 assigned positive charge : 311.8044 centred at (gu) : 89.09438 82.60163 90.18230 assigned negative charge : -309.3048 centred at (gu) : 89.43452 82.90394 90.22242 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 62701 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19356 grid for indexing accessible points = 1.400000 m= 22500 mr = 43288 m= 3598 mr = 16584 m= 218 mr = 2256 m= 2 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 651 time to turn everything in is 0.5700000 number of dielectric boundary points 26803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15578 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) : 0.6290531 object centre at (A) : 20.51150 65.78350 43.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2735614E-02 -1.0390937E-02 midg,1,midg; midg,igrid,midg 7.2862362E-03 7.7241245E-03 1,midg,midg; igrid,midg,midg 1.5630033E-02 -1.9226125E-03 gauss-seidel spectral radius is 0.9985648 estimated iterations to convergence 209 setup time was (sec) 0.8600000 now iterating at: 18:51:43 rms-change max change #iterations 3.667325 172.7440 at 10iterations 1.682939 68.77242 at 20iterations 0.7740899 29.98065 at 30iterations 0.3562489 13.88024 at 40iterations 0.1628229 5.883669 at 50iterations 7.4963138E-02 2.550970 at 60iterations 3.4515936E-02 1.328713 at 70iterations 1.5840922E-02 0.5822163 at 80iterations 7.2820624E-03 0.2500035 at 90iterations 3.3759100E-03 0.1106472 at 100iterations 1.5649103E-03 5.9050560E-02 at 110iterations 7.3277013E-04 2.6522636E-02 at 120iterations finished qdiffx linear iterations at : 18:51:51 total time elapsed so far: 9.270000 # loops : 120 mean,max change (kT/e) : 7.3277013E-04 2.6522636E-02 energy calculations done at 9.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 18:51:52 9.456u 0.323s 0:10.07 97.0% 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 Mon Oct 10 2011 at 18:51:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 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: 2.830739 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): 0.6050001 40.41800 ymin,ymax (A): 37.48700 94.08000 zmin,zma (A): 16.11400 70.88300 x,y,z range (A): 39.81300 56.59300 54.76900 scale (grids/A): 2.830739 object centre (A): 20.51150 65.78350 43.49850 number of atom coordinates read : 2120 total number of charged atoms : 1986 net assigned charge : 2.500004 assigned positive charge : 311.8044 centred at (gu) : 88.64159 78.90228 90.27331 assigned negative charge : -309.3048 centred at (gu) : 89.15171 79.35590 90.33366 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 144845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19356 grid for indexing accessible points = 1.400000 m= 72770 mr = 104785 m= 26486 mr = 59669 m= 6380 mr = 21259 m= 938 mr = 4781 m= 60 mr = 625 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 2172 time to turn everything in is 1.450000 number of dielectric boundary points 60333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 15887 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) : 1.887159 object centre at (A) : 20.51150 65.78350 43.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4790293 -0.1897788 midg,1,midg; midg,igrid,midg 1.6596051E-02 0.2633512 1,midg,midg; igrid,midg,midg 0.1798732 4.2780275E-03 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.780000 now iterating at: 18:51:54 rms-change max change #iterations 8.702573 352.1413 at 10iterations 5.053862 122.0716 at 20iterations 2.906453 60.99099 at 30iterations 1.670465 39.51594 at 40iterations 0.9552866 19.90406 at 50iterations 0.5457241 11.30059 at 60iterations 0.3114437 6.869869 at 70iterations 0.1773615 3.591679 at 80iterations 0.1009082 1.978443 at 90iterations 5.7444043E-02 1.156698 at 100iterations 3.2646913E-02 0.6995773 at 110iterations 1.8575586E-02 0.3865124 at 120iterations 1.0576895E-02 0.2091885 at 130iterations 6.0129054E-03 0.1171494 at 140iterations 3.4317328E-03 6.9454193E-02 at 150iterations 1.9610187E-03 4.1820526E-02 at 160iterations 1.1291226E-03 2.2569656E-02 at 170iterations 6.5468601E-04 1.3517380E-02 at 180iterations finished qdiffx linear iterations at : 18:52:08 total time elapsed so far: 15.50000 # loops : 180 mean,max change (kT/e) : 6.5468601E-04 1.3517380E-02 energy calculations done at 15.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.68000 DelPhi exited at 18:52:08 15.681u 0.325s 0:16.28 98.2% 0+0k 0+0io 0pf+0w