Mon Feb 6 01:01:28 PST 2012 #!/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 Mon Feb 6 2012 at 01:01:28 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: MG4 458 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5937192 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): 21.49900 70.16200 ymin,ymax (A): -26.47500 33.48600 zmin,zma (A): -6.753000 46.02100 x,y,z range (A): 48.66300 59.96100 52.77400 scale (grids/A): 0.5937192 object centre (A): 45.83050 3.505500 19.63400 number of atom coordinates read : 2606 total number of charged atoms : 2463 net assigned charge : 11.00002 assigned positive charge : 395.5995 centred at (gu) : 88.96926 89.67421 90.53307 assigned negative charge : -384.6004 centred at (gu) : 88.87899 89.60804 90.60934 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6059 nv = 96 ne = 84 npr = 51152 no. pairs analyzed = 51152 no. exposed pairs = 3438 no. arc points = 24881 no. surface atoms = 1149 nbur = 1457 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 308 mr = 3059 m= 4 mr = 23 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 0.2200000 number of dielectric boundary points 3289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2560 ## 292 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4318070E-09 1.7855575E-09 midg,1,midg; midg,igrid,midg 2.0397566E-09 5.4179190E-09 1,midg,midg; igrid,midg,midg 1.4391102E-09 5.1796554E-09 gauss-seidel spectral radius is 0.9853276 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 01:01:29 rms-change max change #iterations 0.1040413 17.75141 at 10iterations 8.4219985E-03 1.470741 at 20iterations 7.0463377E-04 0.1097069 at 30iterations 6.0194663E-05 9.2058182E-03 at 40iterations 5.2930936E-06 8.3160400E-04 at 50iterations finished qdiffx linear iterations at : 01:01:32 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.2930936E-06 8.3160400E-04 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 01:01:32 3.509u 0.193s 0:05.06 72.9% 0+0k 0+45848io 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 Feb 6 2012 at 01:01:33 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: MG4 458 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.781158 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): 21.49900 70.16200 ymin,ymax (A): -26.47500 33.48600 zmin,zma (A): -6.753000 46.02100 x,y,z range (A): 48.66300 59.96100 52.77400 scale (grids/A): 1.781158 object centre (A): 45.83050 3.505500 19.63400 number of atom coordinates read : 2606 total number of charged atoms : 2463 net assigned charge : 11.00002 assigned positive charge : 395.5995 centred at (gu) : 86.90699 89.02188 91.59895 assigned negative charge : -384.6004 centred at (gu) : 86.63676 88.82386 91.82795 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24881 grid for indexing accessible points = 1.400000 m= 21688 mr = 43875 m= 2699 mr = 15256 m= 108 mr = 1439 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 180 time to turn everything in is 0.4000000 number of dielectric boundary points 30373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19177 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) : 0.5937192 object centre at (A) : 45.83050 3.505500 19.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4382006E-02 1.1933740E-03 midg,1,midg; midg,igrid,midg 3.2673262E-02 2.9944740E-02 1,midg,midg; igrid,midg,midg 5.6023537E-03 2.1633442E-02 gauss-seidel spectral radius is 0.9984491 estimated iterations to convergence 201 setup time was (sec) 0.6100000 now iterating at: 01:01:34 rms-change max change #iterations 3.711444 175.8976 at 10iterations 1.647761 70.88953 at 20iterations 0.7318959 25.20885 at 30iterations 0.3264851 11.59493 at 40iterations 0.1455512 5.575685 at 50iterations 6.4687289E-02 2.208115 at 60iterations 2.8811224E-02 1.002882 at 70iterations 1.2840514E-02 0.4505615 at 80iterations 5.7282383E-03 0.2309532 at 90iterations 2.5517331E-03 9.4144344E-02 at 100iterations 1.1409356E-03 3.7458420E-02 at 110iterations 5.0518150E-04 1.7685413E-02 at 120iterations finished qdiffx linear iterations at : 01:01:41 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 5.0518150E-04 1.7685413E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 01:01:42 7.948u 0.223s 0:08.78 92.9% 0+0k 0+45248io 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 Feb 6 2012 at 01:01:42 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: MG4 458 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.671737 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): 21.49900 70.16200 ymin,ymax (A): -26.47500 33.48600 zmin,zma (A): -6.753000 46.02100 x,y,z range (A): 48.66300 59.96100 52.77400 scale (grids/A): 2.671737 object centre (A): 45.83050 3.505500 19.63400 number of atom coordinates read : 2606 total number of charged atoms : 2463 net assigned charge : 11.00002 assigned positive charge : 395.5995 centred at (gu) : 85.36033 88.53260 92.39822 assigned negative charge : -384.6004 centred at (gu) : 84.95503 88.23573 92.74185 start vw surface at 0.1200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 153762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24881 grid for indexing accessible points = 1.400000 m= 72369 mr = 106831 m= 23029 mr = 57559 m= 4477 mr = 17814 m= 484 mr = 3094 m= 25 mr = 261 m= 0 mr = 8 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 669 time to turn everything in is 1.050000 number of dielectric boundary points 68579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 19700 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) : 1.781158 object centre at (A) : 45.83050 3.505500 19.63400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1326598 -1.1587124E-02 midg,1,midg; midg,igrid,midg 0.2840049 0.5247875 1,midg,midg; igrid,midg,midg 5.0326005E-02 0.2312561 gauss-seidel spectral radius is 0.9992129 estimated iterations to convergence 281 setup time was (sec) 1.270000 now iterating at: 01:01:43 rms-change max change #iterations 9.067383 295.9461 at 10iterations 5.219389 133.6018 at 20iterations 2.979728 65.65021 at 30iterations 1.690196 32.80679 at 40iterations 0.9578363 20.02418 at 50iterations 0.5421853 11.69809 at 60iterations 0.3065172 6.423135 at 70iterations 0.1729329 3.463733 at 80iterations 9.7473122E-02 1.940544 at 90iterations 5.5055659E-02 1.071457 at 100iterations 3.1038176E-02 0.5976372 at 110iterations 1.7558670E-02 0.3653088 at 120iterations 9.8644150E-03 0.1864281 at 130iterations 5.5777589E-03 0.1134911 at 140iterations 3.1430249E-03 6.2898636E-02 at 150iterations 1.7697305E-03 3.6235809E-02 at 160iterations 9.9856954E-04 2.3591995E-02 at 170iterations 5.6427997E-04 1.0383606E-02 at 180iterations finished qdiffx linear iterations at : 01:01:55 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 5.6427997E-04 1.0383606E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 01:01:55 12.745u 0.221s 0:13.29 97.5% 0+0k 0+45240io 0pf+0w