Sun Oct 9 06:39:43 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+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 Sun Oct 9 2011 at 06:39:43 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: 262 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 : 362.1562 centred at (gu) : 90.53622 89.20355 90.37643 assigned negative charge : -365.1568 centred at (gu) : 90.61775 89.10071 90.33432 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 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 = 0.1000000 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 = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 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 0.4100000 number of grid points assigned charge 7181 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5425058E-09 1.6147904E-10 midg,1,midg; midg,igrid,midg -3.6432044E-09 1.1872239E-09 1,midg,midg; igrid,midg,midg 8.6525243E-10 -2.8900751E-09 gauss-seidel spectral radius is 0.9849169 estimated iterations to convergence 67 setup time was (sec) 0.5400000 now iterating at: 06:39:44 rms-change max change #iterations 9.2301756E-02 14.61401 at 10iterations 7.3860064E-03 1.207129 at 20iterations 5.9365068E-04 9.6792221E-02 at 30iterations 4.7264868E-05 8.4896088E-03 at 40iterations 3.7389320E-06 6.6566467E-04 at 50iterations finished qdiffx linear iterations at : 06:39:46 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.7389320E-06 6.6566467E-04 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 06:39:47 3.428u 0.197s 0:03.90 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 06:39:47 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: 262 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= 7.0000000E-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 : 362.1562 centred at (gu) : 91.60829 87.61036 91.12895 assigned negative charge : -365.1568 centred at (gu) : 91.85311 87.30208 91.00282 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 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 = 0.2000000 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 0.5800000 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 -2.4099866E-02 7.1342411E-03 midg,1,midg; midg,igrid,midg -3.4925412E-02 -1.5021736E-03 1,midg,midg; igrid,midg,midg -8.9892093E-03 -1.4994763E-02 gauss-seidel spectral radius is 0.9984068 estimated iterations to convergence 199 setup time was (sec) 0.7600000 now iterating at: 06:39:48 rms-change max change #iterations 3.484007 173.5386 at 10iterations 1.518928 72.39552 at 20iterations 0.6653892 24.29267 at 30iterations 0.2916908 11.68338 at 40iterations 0.1283043 4.298546 at 50iterations 5.6275748E-02 2.189377 at 60iterations 2.4715561E-02 0.8654652 at 70iterations 1.0830134E-02 0.3973541 at 80iterations 4.7451486E-03 0.1603231 at 90iterations 2.0954623E-03 7.9212666E-02 at 100iterations 9.2052302E-04 3.3967972E-02 at 110iterations 4.0487820E-04 1.5460014E-02 at 120iterations finished qdiffx linear iterations at : 06:39:56 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 4.0487820E-04 1.5460014E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.990000 DelPhi exited at 06:39:56 8.997u 0.261s 0:09.55 96.8% 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 06:39:56 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: 262 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= 7.0000000E-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 : 362.1562 centred at (gu) : 92.41233 86.41543 91.69325 assigned negative charge : -365.1568 centred at (gu) : 92.77958 85.95303 91.50420 start vw surface at 0.1500000 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 = 0.5799999 no. cavity mid-points inaccessible to solvent = 2305 time to turn everything in is 1.050000 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 1.170000 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 -0.4257116 0.2476821 midg,1,midg; midg,igrid,midg -0.5425780 -5.4836604E-03 1,midg,midg; igrid,midg,midg -0.1859634 -0.1859725 gauss-seidel spectral radius is 0.9992072 estimated iterations to convergence 280 setup time was (sec) 1.320000 now iterating at: 06:39:58 rms-change max change #iterations 8.628176 321.5617 at 10iterations 4.987398 157.7172 at 20iterations 2.853279 73.48759 at 30iterations 1.623888 39.31552 at 40iterations 0.9227901 28.34933 at 50iterations 0.5240234 11.82063 at 60iterations 0.2960489 6.257284 at 70iterations 0.1674209 4.182322 at 80iterations 9.4495587E-02 1.999367 at 90iterations 5.3272415E-02 1.052795 at 100iterations 3.0004680E-02 0.6027813 at 110iterations 1.6920460E-02 0.3374090 at 120iterations 9.5198127E-03 0.1911588 at 130iterations 5.3557465E-03 0.1101608 at 140iterations 3.0168346E-03 6.2458038E-02 at 150iterations 1.6949102E-03 3.3919096E-02 at 160iterations 9.5317635E-04 1.8886566E-02 at 170iterations 5.3739961E-04 1.1024475E-02 at 180iterations finished qdiffx linear iterations at : 06:40:07 total time elapsed so far: 10.79000 # loops : 180 mean,max change (kT/e) : 5.3739961E-04 1.1024475E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 06:40:08 10.966u 0.178s 0:11.41 97.5% 0+0k 0+0io 0pf+0w