Mon Oct 10 17:05:09 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 Mon Oct 10 2011 at 17:05:09 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: GLM 254 has a net charge of -0.0940 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: 0.5688627 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): -8.366000 54.21500 ymin,ymax (A): -13.45600 33.83700 zmin,zma (A): -17.94600 35.97600 x,y,z range (A): 62.58100 47.29300 53.92200 scale (grids/A): 0.5688627 object centre (A): 22.92450 10.19050 9.015000 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.920027 assigned positive charge : 408.4207 centred at (gu) : 89.30373 89.96095 89.84859 assigned negative charge : -403.5014 centred at (gu) : 89.44896 89.96808 89.85342 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5770 nv = 96 ne = 84 npr = 55211 no. pairs analyzed = 55211 no. exposed pairs = 3690 no. arc points = 25608 no. surface atoms = 1244 nbur = 1489 mkacc time = 0.1400000 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= 248 mr = 2832 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2667 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0411033E-10 6.2203970E-10 midg,1,midg; midg,igrid,midg 8.1538015E-10 6.0682576E-10 1,midg,midg; igrid,midg,midg 3.1546068E-09 -1.1088336E-09 gauss-seidel spectral radius is 0.9840392 estimated iterations to convergence 65 setup time was (sec) 0.6000000 now iterating at: 17:05:10 rms-change max change #iterations 8.0642141E-02 13.17033 at 10iterations 6.1863381E-03 1.033019 at 20iterations 4.8171962E-04 7.8399658E-02 at 30iterations 6.0063303E-05 8.7223053E-03 at 40iterations 1.4976657E-05 2.1142960E-03 at 50iterations finished qdiffx linear iterations at : 17:05:13 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 1.4976657E-05 2.1142960E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 17:05:14 4.654u 0.384s 0:05.73 87.7% 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 Mon Oct 10 2011 at 17:05:14 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: GLM 254 has a net charge of -0.0940 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: 1.706588 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): -8.366000 54.21500 ymin,ymax (A): -13.45600 33.83700 zmin,zma (A): -17.94600 35.97600 x,y,z range (A): 62.58100 47.29300 53.92200 scale (grids/A): 1.706588 object centre (A): 22.92450 10.19050 9.015000 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.920027 assigned positive charge : 408.4207 centred at (gu) : 87.91069 89.88217 89.54506 assigned negative charge : -403.5014 centred at (gu) : 88.34658 89.90380 89.56010 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63304 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25608 grid for indexing accessible points = 1.400000 m= 19549 mr = 41618 m= 2311 mr = 12996 m= 76 mr = 1124 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 29500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 20026 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) : 0.5688627 object centre at (A) : 22.92450 10.19050 9.015000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7773245E-03 5.6520095E-03 midg,1,midg; midg,igrid,midg 6.9099478E-04 2.6555953E-03 1,midg,midg; igrid,midg,midg 3.0520065E-02 -4.5087556E-03 gauss-seidel spectral radius is 0.9983316 estimated iterations to convergence 194 setup time was (sec) 0.8400000 now iterating at: 17:05:16 rms-change max change #iterations 3.485272 162.9413 at 10iterations 1.506533 57.62129 at 20iterations 0.6518403 23.55876 at 30iterations 0.2817660 10.46454 at 40iterations 0.1221166 4.406986 at 50iterations 5.2898433E-02 1.839172 at 60iterations 2.2939270E-02 0.7968178 at 70iterations 9.9245049E-03 0.3905058 at 80iterations 4.3332363E-03 0.1587067 at 90iterations 1.8938384E-03 6.3113213E-02 at 100iterations 8.3440181E-04 3.0154228E-02 at 110iterations 3.7876965E-04 1.3336182E-02 at 120iterations finished qdiffx linear iterations at : 17:05:26 total time elapsed so far: 11.25000 # loops : 120 mean,max change (kT/e) : 3.7876965E-04 1.3336182E-02 energy calculations done at 11.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 17:05:27 11.434u 0.442s 0:12.46 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 Mon Oct 10 2011 at 17:05:27 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 83 has a net charge of 0.5140 !!! WARNING: GLM 254 has a net charge of -0.0940 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: 2.559882 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): -8.366000 54.21500 ymin,ymax (A): -13.45600 33.83700 zmin,zma (A): -17.94600 35.97600 x,y,z range (A): 62.58100 47.29300 53.92200 scale (grids/A): 2.559882 object centre (A): 22.92450 10.19050 9.015000 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.920027 assigned positive charge : 408.4207 centred at (gu) : 86.86591 89.82311 89.31750 assigned negative charge : -403.5014 centred at (gu) : 87.52000 89.85571 89.34004 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 146674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25608 grid for indexing accessible points = 1.400000 m= 66193 mr = 102309 m= 20164 mr = 51016 m= 3713 mr = 14711 m= 287 mr = 2375 m= 9 mr = 110 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 66519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 20700 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) : 1.706588 object centre at (A) : 22.92450 10.19050 9.015000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5853388E-02 8.5033849E-02 midg,1,midg; midg,igrid,midg 8.0278842E-04 2.7572997E-02 1,midg,midg; igrid,midg,midg 0.4863829 -3.8957749E-02 gauss-seidel spectral radius is 0.9991853 estimated iterations to convergence 277 setup time was (sec) 1.630000 now iterating at: 17:05:29 rms-change max change #iterations 8.826941 310.4635 at 10iterations 5.041647 122.9798 at 20iterations 2.861261 73.39087 at 30iterations 1.622530 37.40168 at 40iterations 0.9144267 19.80956 at 50iterations 0.5149195 10.44940 at 60iterations 0.2897297 6.170891 at 70iterations 0.1624063 3.287529 at 80iterations 9.0961277E-02 1.986862 at 90iterations 5.1048115E-02 1.113364 at 100iterations 2.8589781E-02 0.6330566 at 110iterations 1.5999261E-02 0.3156171 at 120iterations 8.9683514E-03 0.1859884 at 130iterations 5.0223167E-03 0.1077309 at 140iterations 2.8261517E-03 6.0477257E-02 at 150iterations 1.6031181E-03 3.4599304E-02 at 160iterations 9.1311993E-04 1.9632339E-02 at 170iterations 5.3053012E-04 1.1067867E-02 at 180iterations finished qdiffx linear iterations at : 17:05:46 total time elapsed so far: 18.99000 # loops : 180 mean,max change (kT/e) : 5.3053012E-04 1.1067867E-02 energy calculations done at 18.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.16000 DelPhi exited at 17:05:47 19.167u 0.477s 0:20.03 98.0% 0+0k 0+0io 0pf+0w