Wed Dec 28 11:03:05 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 11:03:05 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6478853 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): -6.227000 30.89700 ymin,ymax (A): -46.66200 7.556000 zmin,zma (A): -54.51700 0.4310000 x,y,z range (A): 37.12400 54.21800 54.94800 scale (grids/A): 0.6478853 object centre (A): 12.33500 -19.55300 -27.04300 number of atom coordinates read : 1953 total number of charged atoms : 1820 net assigned charge : 2.681006 assigned positive charge : 291.4019 centred at (gu) : 90.07458 92.12072 89.82378 assigned negative charge : -288.7212 centred at (gu) : 89.96140 92.27076 89.90662 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5718 nv = 96 ne = 84 npr = 39334 no. pairs analyzed = 39334 no. exposed pairs = 2557 no. arc points = 17714 no. surface atoms = 867 nbur = 1086 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 321 mr = 3136 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1760 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6583 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4530289E-08 -3.5329548E-09 midg,1,midg; midg,igrid,midg 1.3438996E-08 -1.7758154E-08 1,midg,midg; igrid,midg,midg -6.8717254E-09 1.7442620E-08 gauss-seidel spectral radius is 0.9876012 estimated iterations to convergence 73 setup time was (sec) 0.7300000 now iterating at: 11:03:07 rms-change max change #iterations 0.1329236 19.31841 at 10iterations 1.3429790E-02 1.973382 at 20iterations 1.3847328E-03 0.2029305 at 30iterations 1.4087738E-04 2.5145531E-02 at 40iterations 1.4056591E-05 2.5033951E-03 at 50iterations finished qdiffx linear iterations at : 11:03:13 total time elapsed so far: 7.260000 # loops : 50 mean,max change (kT/e) : 1.4056591E-05 2.5033951E-03 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.480000 DelPhi exited at 11:03:14 7.488u 0.740s 0:09.00 91.3% 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 11:03:14 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASH 25 has a net charge of -0.3190 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: 1.943656 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): -6.227000 30.89700 ymin,ymax (A): -46.66200 7.556000 zmin,zma (A): -54.51700 0.4310000 x,y,z range (A): 37.12400 54.21800 54.94800 scale (grids/A): 1.943656 object centre (A): 12.33500 -19.55300 -27.04300 number of atom coordinates read : 1953 total number of charged atoms : 1820 net assigned charge : 2.681006 assigned positive charge : 291.4019 centred at (gu) : 90.22392 96.36237 89.47112 assigned negative charge : -288.7212 centred at (gu) : 89.88425 96.81253 89.71995 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 61029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 22796 mr = 41756 m= 3674 mr = 17158 m= 231 mr = 2362 m= 6 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 261 time to turn everything in is 0.7000000 number of dielectric boundary points 26368 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14357 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) : 0.6478853 object centre at (A) : 12.33500 -19.55300 -27.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7839758E-03 4.6438284E-02 midg,1,midg; midg,igrid,midg 4.1044801E-02 -1.9667851E-02 1,midg,midg; igrid,midg,midg -4.3558776E-03 8.2776919E-03 gauss-seidel spectral radius is 0.9986156 estimated iterations to convergence 213 setup time was (sec) 1.100000 now iterating at: 11:03:16 rms-change max change #iterations 3.784485 198.6144 at 10iterations 1.764254 69.69560 at 20iterations 0.8241823 30.50307 at 30iterations 0.3823162 14.02536 at 40iterations 0.1780251 5.982869 at 50iterations 8.2514457E-02 2.863857 at 60iterations 3.8423348E-02 1.299361 at 70iterations 1.7876033E-02 0.6583405 at 80iterations 8.3060553E-03 0.2986145 at 90iterations 3.8712688E-03 0.1496477 at 100iterations 1.7997893E-03 6.3117027E-02 at 110iterations 8.4017689E-04 2.7894497E-02 at 120iterations finished qdiffx linear iterations at : 11:03:32 total time elapsed so far: 17.44000 # loops : 120 mean,max change (kT/e) : 8.4017689E-04 2.7894497E-02 energy calculations done at 17.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.67000 DelPhi exited at 11:03:34 17.671u 0.616s 0:19.10 95.7% 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 11:03:34 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1953 !!! WARNING: ASH 25 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.915484 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): -6.227000 30.89700 ymin,ymax (A): -46.66200 7.556000 zmin,zma (A): -54.51700 0.4310000 x,y,z range (A): 37.12400 54.21800 54.94800 scale (grids/A): 2.915484 object centre (A): 12.33500 -19.55300 -27.04300 number of atom coordinates read : 1953 total number of charged atoms : 1820 net assigned charge : 2.681006 assigned positive charge : 291.4019 centred at (gu) : 90.33584 99.54346 89.20659 assigned negative charge : -288.7212 centred at (gu) : 89.82652 100.2189 89.57993 start vw surface at 0.1300000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 140731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17714 grid for indexing accessible points = 1.400000 m= 72725 mr = 100900 m= 27306 mr = 59975 m= 6728 mr = 22441 m= 992 mr = 5174 m= 60 mr = 713 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 822 time to turn everything in is 1.850000 number of dielectric boundary points 59309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 14560 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) : 1.943656 object centre at (A) : 12.33500 -19.55300 -27.04300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9763876E-02 0.8765618 midg,1,midg; midg,igrid,midg 0.4097890 -0.2856783 1,midg,midg; igrid,midg,midg -3.7823908E-02 5.0436780E-02 gauss-seidel spectral radius is 0.9992439 estimated iterations to convergence 287 setup time was (sec) 2.380000 now iterating at: 11:03:37 rms-change max change #iterations 8.835003 390.1045 at 10iterations 5.080256 132.5138 at 20iterations 2.910033 57.26587 at 30iterations 1.665293 37.51889 at 40iterations 0.9486696 20.14616 at 50iterations 0.5419444 10.91331 at 60iterations 0.3093063 6.166965 at 70iterations 0.1759957 3.397125 at 80iterations 0.1003615 1.923922 at 90iterations 5.7143450E-02 1.152008 at 100iterations 3.2518178E-02 0.6609669 at 110iterations 1.8603345E-02 0.3573999 at 120iterations 1.0562228E-02 0.2093793 at 130iterations 6.0237725E-03 0.1185226 at 140iterations 3.4424460E-03 7.5773239E-02 at 150iterations 1.9540365E-03 3.9749146E-02 at 160iterations 1.1125649E-03 1.9865036E-02 at 170iterations 6.3545525E-04 1.1821747E-02 at 180iterations finished qdiffx linear iterations at : 11:04:03 total time elapsed so far: 28.67000 # loops : 180 mean,max change (kT/e) : 6.3545525E-04 1.1821747E-02 energy calculations done at 28.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.89000 DelPhi exited at 11:04:04 28.893u 0.904s 0:30.53 97.5% 0+0k 0+0io 0pf+0w