Sun Oct 9 22:48:13 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 Sun Oct 9 2011 at 22:48:13 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 = 2185 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6525525 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): 12.09700 66.12500 ymin,ymax (A): -11.99500 31.06900 zmin,zma (A): -11.35700 43.19800 x,y,z range (A): 54.02800 43.06400 54.55500 scale (grids/A): 0.6525525 object centre (A): 39.11100 9.537000 15.92050 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 4.499999 assigned positive charge : 324.1685 centred at (gu) : 89.13405 91.77330 90.22494 assigned negative charge : -319.6689 centred at (gu) : 89.33155 91.69563 90.02265 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6373 nv = 96 ne = 84 npr = 42595 no. pairs analyzed = 42595 no. exposed pairs = 2863 no. arc points = 20334 no. surface atoms = 969 nbur = 1216 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3369 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1954 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7443 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7950601E-08 3.7060243E-08 midg,1,midg; midg,igrid,midg -1.0085939E-09 2.7831765E-08 1,midg,midg; igrid,midg,midg 4.1733809E-08 -1.5040705E-08 gauss-seidel spectral radius is 0.9877996 estimated iterations to convergence 74 setup time was (sec) 0.5000000 now iterating at: 22:48:14 rms-change max change #iterations 0.1422811 23.04071 at 10iterations 1.4775011E-02 2.097860 at 20iterations 1.5565845E-03 0.2171135 at 30iterations 2.1536452E-04 3.7153244E-02 at 40iterations 6.2544568E-05 1.2310982E-02 at 50iterations finished qdiffx linear iterations at : 22:48:16 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 6.2544568E-05 1.2310982E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.260000 DelPhi exited at 22:48:17 3.260u 0.210s 0:03.75 92.5% 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 22:48:17 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 = 2185 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.957657 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): 12.09700 66.12500 ymin,ymax (A): -11.99500 31.06900 zmin,zma (A): -11.35700 43.19800 x,y,z range (A): 54.02800 43.06400 54.55500 scale (grids/A): 1.957657 object centre (A): 39.11100 9.537000 15.92050 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 4.499999 assigned positive charge : 324.1685 centred at (gu) : 87.40181 95.31972 90.67442 assigned negative charge : -319.6689 centred at (gu) : 87.99477 95.08688 90.06783 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 68582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20334 grid for indexing accessible points = 1.400000 m= 24167 mr = 46286 m= 4113 mr = 17545 m= 308 mr = 2676 m= 2 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 30524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16149 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) : 0.6525525 object centre at (A) : 39.11100 9.537000 15.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4446199E-02 1.1766698E-02 midg,1,midg; midg,igrid,midg -8.7760100E-03 1.0985460E-02 1,midg,midg; igrid,midg,midg 3.0620549E-02 1.9946126E-02 gauss-seidel spectral radius is 0.9986720 estimated iterations to convergence 217 setup time was (sec) 0.7800000 now iterating at: 22:48:18 rms-change max change #iterations 4.003012 208.1579 at 10iterations 1.898064 79.10094 at 20iterations 0.9003762 28.82295 at 30iterations 0.4238928 15.19013 at 40iterations 0.2003582 6.780414 at 50iterations 9.5164038E-02 3.588683 at 60iterations 4.4968270E-02 1.416824 at 70iterations 2.1302424E-02 0.7302513 at 80iterations 1.0154184E-02 0.3504066 at 90iterations 4.8745112E-03 0.1774368 at 100iterations 2.3987433E-03 8.2523346E-02 at 110iterations 1.2295686E-03 4.8267365E-02 at 120iterations finished qdiffx linear iterations at : 22:48:24 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.2295686E-03 4.8267365E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 22:48:25 7.411u 0.246s 0:08.03 95.2% 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 22:48:25 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 = 2185 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.936486 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): 12.09700 66.12500 ymin,ymax (A): -11.99500 31.06900 zmin,zma (A): -11.35700 43.19800 x,y,z range (A): 54.02800 43.06400 54.55500 scale (grids/A): 2.936486 object centre (A): 39.11100 9.537000 15.92050 number of atom coordinates read : 2185 total number of charged atoms : 2046 net assigned charge : 4.499999 assigned positive charge : 324.1685 centred at (gu) : 86.10263 97.97941 91.01168 assigned negative charge : -319.6689 centred at (gu) : 86.99216 97.63030 90.10160 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 158487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20334 grid for indexing accessible points = 1.400000 m= 78266 mr = 112361 m= 28275 mr = 63425 m= 7402 mr = 22505 m= 1282 mr = 5585 m= 118 mr = 922 m= 1 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 68959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 16368 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) : 1.957657 object centre at (A) : 39.11100 9.537000 15.92050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2927604E-02 -7.6773949E-02 midg,1,midg; midg,igrid,midg -0.1487554 0.1035984 1,midg,midg; igrid,midg,midg 0.1599236 0.5170295 gauss-seidel spectral radius is 0.9992667 estimated iterations to convergence 291 setup time was (sec) 1.530000 now iterating at: 22:48:27 rms-change max change #iterations 9.423200 398.1185 at 10iterations 5.541223 168.6369 at 20iterations 3.241070 74.62912 at 30iterations 1.891631 40.26636 at 40iterations 1.101285 24.79713 at 50iterations 0.6392326 12.95552 at 60iterations 0.3700499 8.292942 at 70iterations 0.2148416 4.154488 at 80iterations 0.1243172 2.535095 at 90iterations 7.2022684E-02 1.522943 at 100iterations 4.1513588E-02 0.7752829 at 110iterations 2.4043553E-02 0.4958191 at 120iterations 1.3867380E-02 0.2698102 at 130iterations 7.9985382E-03 0.1510072 at 140iterations 4.6339221E-03 9.7355843E-02 at 150iterations 2.6680196E-03 5.2263260E-02 at 160iterations 1.5374272E-03 2.8140068E-02 at 170iterations 8.8988600E-04 1.6887665E-02 at 180iterations finished qdiffx linear iterations at : 22:48:37 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 8.8988600E-04 1.6887665E-02 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 22:48:38 11.918u 0.262s 0:12.54 97.0% 0+0k 0+0io 0pf+0w