Sun Oct 9 06:39:16 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 06:39:16 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 = 2436 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 has a net charge of -2.0000 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: 0.5855552 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): -27.97800 32.81900 ymin,ymax (A): -0.6060000 57.68300 zmin,zma (A): -27.20300 29.33500 x,y,z range (A): 60.79700 58.28900 56.53800 scale (grids/A): 0.5855552 object centre (A): 2.420500 28.53850 1.065999 number of atom coordinates read : 2436 total number of charged atoms : 2292 net assigned charge : -2.999984 assigned positive charge : 360.5562 centred at (gu) : 90.54008 89.21272 90.39160 assigned negative charge : -363.5568 centred at (gu) : 90.61818 89.10596 90.35126 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5825 nv = 96 ne = 84 npr = 47021 no. pairs analyzed = 47021 no. exposed pairs = 3470 no. arc points = 26204 no. surface atoms = 1158 nbur = 1278 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 253 mr = 2735 m= 1 mr = 7 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 3337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2694 ## 335 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7181 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4982319E-09 1.1634313E-10 midg,1,midg; midg,igrid,midg -3.7275596E-09 1.2502283E-09 1,midg,midg; igrid,midg,midg 7.9366896E-10 -2.7978397E-09 gauss-seidel spectral radius is 0.9849169 estimated iterations to convergence 67 setup time was (sec) 0.5100000 now iterating at: 06:39:17 rms-change max change #iterations 9.1153465E-02 14.61401 at 10iterations 7.2869784E-03 1.235950 at 20iterations 5.8534212E-04 9.1529846E-02 at 30iterations 4.6668396E-05 8.2359314E-03 at 40iterations 3.6791700E-06 6.5803528E-04 at 50iterations finished qdiffx linear iterations at : 06:39:20 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 3.6791700E-06 6.5803528E-04 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 06:39:20 3.106u 0.130s 0:03.53 91.5% 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 06:39:20 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 = 2436 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 has a net charge of -2.0000 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: 1.756666 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): -27.97800 32.81900 ymin,ymax (A): -0.6060000 57.68300 zmin,zma (A): -27.20300 29.33500 x,y,z range (A): 60.79700 58.28900 56.53800 scale (grids/A): 1.756666 object centre (A): 2.420500 28.53850 1.065999 number of atom coordinates read : 2436 total number of charged atoms : 2292 net assigned charge : -2.999984 assigned positive charge : 360.5562 centred at (gu) : 91.61990 87.63785 91.17448 assigned negative charge : -363.5568 centred at (gu) : 91.85436 87.31786 91.05370 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 62533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26204 grid for indexing accessible points = 1.400000 m= 19436 mr = 39140 m= 2247 mr = 13119 m= 77 mr = 1113 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 593 time to turn everything in is 0.4700000 number of dielectric boundary points 30918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 264 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 17852 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) : 0.5855552 object centre at (A) : 2.420500 28.53850 1.065999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3773715E-02 7.0682419E-03 midg,1,midg; midg,igrid,midg -3.5444766E-02 -1.3515118E-03 1,midg,midg; igrid,midg,midg -9.2161512E-03 -1.4745875E-02 gauss-seidel spectral radius is 0.9984068 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 06:39:21 rms-change max change #iterations 3.464368 173.5386 at 10iterations 1.510468 72.40483 at 20iterations 0.6615609 24.09640 at 30iterations 0.2900215 11.73492 at 40iterations 0.1275476 4.317700 at 50iterations 5.5954900E-02 2.196974 at 60iterations 2.4572248E-02 0.8937683 at 70iterations 1.0766802E-02 0.3922577 at 80iterations 4.7166809E-03 0.1605389 at 90iterations 2.0825858E-03 7.6654911E-02 at 100iterations 9.1488217E-04 3.3403397E-02 at 110iterations 4.0235865E-04 1.5260696E-02 at 120iterations finished qdiffx linear iterations at : 06:39:29 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 4.0235865E-04 1.5260696E-02 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 06:39:30 8.968u 0.240s 0:09.51 96.7% 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 Sun Oct 9 2011 at 06:39:30 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 = 2436 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: ASP 372 has a net charge of -2.0000 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: 2.634998 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): -27.97800 32.81900 ymin,ymax (A): -0.6060000 57.68300 zmin,zma (A): -27.20300 29.33500 x,y,z range (A): 60.79700 58.28900 56.53800 scale (grids/A): 2.634998 object centre (A): 2.420500 28.53850 1.065999 number of atom coordinates read : 2436 total number of charged atoms : 2292 net assigned charge : -2.999984 assigned positive charge : 360.5562 centred at (gu) : 92.42976 86.45667 91.76158 assigned negative charge : -363.5568 centred at (gu) : 92.78146 85.97671 91.58048 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 144283 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26204 grid for indexing accessible points = 1.400000 m= 65899 mr = 96093 m= 19657 mr = 51003 m= 3702 mr = 14549 m= 344 mr = 2411 m= 4 mr = 137 m= 0 mr = 0 time to grow re-entrant surface = 0.5999999 no. cavity mid-points inaccessible to solvent = 2305 time to turn everything in is 1.090000 number of dielectric boundary points 69696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 18331 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) : 1.756666 object centre at (A) : 2.420500 28.53850 1.065999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4214385 0.2470538 midg,1,midg; midg,igrid,midg -0.5497921 -3.5636697E-03 1,midg,midg; igrid,midg,midg -0.1884773 -0.1827919 gauss-seidel spectral radius is 0.9992072 estimated iterations to convergence 280 setup time was (sec) 1.400000 now iterating at: 06:39:31 rms-change max change #iterations 8.584665 321.5595 at 10iterations 4.962992 157.7126 at 20iterations 2.839858 73.48781 at 30iterations 1.616036 39.57176 at 40iterations 0.9186671 27.90917 at 50iterations 0.5217170 11.88015 at 60iterations 0.2948275 6.209682 at 70iterations 0.1667370 4.163475 at 80iterations 9.4123550E-02 2.000992 at 90iterations 5.3065538E-02 1.051292 at 100iterations 2.9884728E-02 0.6027641 at 110iterations 1.6854219E-02 0.3364505 at 120iterations 9.4840033E-03 0.1917334 at 130iterations 5.3350292E-03 0.1098623 at 140iterations 3.0051265E-03 6.2564850E-02 at 150iterations 1.6882335E-03 3.4000039E-02 at 160iterations 9.4946317E-04 1.8840790E-02 at 170iterations 5.3533155E-04 1.0687828E-02 at 180iterations finished qdiffx linear iterations at : 06:39:42 total time elapsed so far: 12.23000 # loops : 180 mean,max change (kT/e) : 5.3533155E-04 1.0687828E-02 energy calculations done at 12.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 06:39:43 12.403u 0.266s 0:13.00 97.3% 0+0k 0+0io 0pf+0w