Mon Oct 10 09:47:53 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 Mon Oct 10 2011 at 09:47:53 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 = 2932 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: 0.5497221 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): 111.6850 176.4450 ymin,ymax (A): -42.55600 10.41100 zmin,zma (A): 47.20200 104.9590 x,y,z range (A): 64.75999 52.96700 57.75700 scale (grids/A): 0.5497221 object centre (A): 144.0650 -16.07250 76.08050 number of atom coordinates read : 2932 total number of charged atoms : 2780 net assigned charge : 8.000021 assigned positive charge : 428.7507 centred at (gu) : 90.44617 88.90366 89.58736 assigned negative charge : -420.7513 centred at (gu) : 90.49105 88.98092 89.42655 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6052 nv = 96 ne = 84 npr = 55678 no. pairs analyzed = 55678 no. exposed pairs = 4371 no. arc points = 32675 no. surface atoms = 1441 nbur = 1491 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 = 1.540000 m= 273 mr = 2667 m= 3 mr = 6 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 0.3300000 number of dielectric boundary points 3655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3223 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7767 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7724276E-10 1.5494757E-09 midg,1,midg; midg,igrid,midg 1.4786399E-09 1.6159343E-11 1,midg,midg; igrid,midg,midg 8.0701928E-10 2.7740185E-10 gauss-seidel spectral radius is 0.9829556 estimated iterations to convergence 63 setup time was (sec) 0.5600000 now iterating at: 09:47:54 rms-change max change #iterations 7.2645403E-02 11.36442 at 10iterations 4.9444484E-03 0.9305954 at 20iterations 3.3287838E-04 5.2816749E-02 at 30iterations 2.4652716E-05 3.8061142E-03 at 40iterations 2.4734361E-06 3.1852722E-04 at 50iterations finished qdiffx linear iterations at : 09:47:57 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.4734361E-06 3.1852722E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:47:57 3.374u 0.154s 0:03.81 92.3% 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 Mon Oct 10 2011 at 09:47:57 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 = 2932 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.649166 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): 111.6850 176.4450 ymin,ymax (A): -42.55600 10.41100 zmin,zma (A): 47.20200 104.9590 x,y,z range (A): 64.75999 52.96700 57.75700 scale (grids/A): 1.649166 object centre (A): 144.0650 -16.07250 76.08050 number of atom coordinates read : 2932 total number of charged atoms : 2780 net assigned charge : 8.000021 assigned positive charge : 428.7507 centred at (gu) : 91.33769 86.71062 88.76154 assigned negative charge : -420.7513 centred at (gu) : 91.47283 86.94246 88.27928 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 64773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32675 grid for indexing accessible points = 1.400000 m= 20346 mr = 39332 m= 2304 mr = 13154 m= 67 mr = 1047 m= 0 mr = 10 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 33947 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 365 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21348 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) : 0.5497221 object centre at (A) : 144.0650 -16.07250 76.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8259926E-03 2.5135726E-02 midg,1,midg; midg,igrid,midg 1.3577044E-02 2.3306054E-03 1,midg,midg; igrid,midg,midg 1.1292639E-02 -2.7779865E-03 gauss-seidel spectral radius is 0.9982497 estimated iterations to convergence 190 setup time was (sec) 0.8600000 now iterating at: 09:47:58 rms-change max change #iterations 3.292641 166.0638 at 10iterations 1.392272 62.88871 at 20iterations 0.5875834 24.33384 at 30iterations 0.2474979 9.133978 at 40iterations 0.1046180 4.064936 at 50iterations 4.3982767E-02 1.697601 at 60iterations 1.8654123E-02 0.7856941 at 70iterations 7.8640068E-03 0.2882996 at 80iterations 3.3306940E-03 0.1240432 at 90iterations 1.4059220E-03 5.9135437E-02 at 100iterations 5.9560762E-04 2.1847725E-02 at 110iterations 2.5168786E-04 1.0002136E-02 at 120iterations finished qdiffx linear iterations at : 09:48:05 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 2.5168786E-04 1.0002136E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 09:48:06 8.267u 0.250s 0:08.83 96.3% 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 Mon Oct 10 2011 at 09:48:06 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 = 2932 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: 2.473749 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): 111.6850 176.4450 ymin,ymax (A): -42.55600 10.41100 zmin,zma (A): 47.20200 104.9590 x,y,z range (A): 64.75999 52.96700 57.75700 scale (grids/A): 2.473749 object centre (A): 144.0650 -16.07250 76.08050 number of atom coordinates read : 2932 total number of charged atoms : 2780 net assigned charge : 8.000021 assigned positive charge : 428.7507 centred at (gu) : 92.00629 85.06574 88.14233 assigned negative charge : -420.7513 centred at (gu) : 92.20918 85.41375 87.41881 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 149836 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32675 grid for indexing accessible points = 1.400000 m= 67394 mr = 97086 m= 20807 mr = 50885 m= 3438 mr = 14975 m= 257 mr = 2118 m= 2 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.210000 number of dielectric boundary points 76553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 22222 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) : 1.649166 object centre at (A) : 144.0650 -16.07250 76.08050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1680302E-02 0.4311879 midg,1,midg; midg,igrid,midg 0.1755890 4.2469043E-02 1,midg,midg; igrid,midg,midg 0.1413870 -0.1197314 gauss-seidel spectral radius is 0.9991768 estimated iterations to convergence 275 setup time was (sec) 1.550000 now iterating at: 09:48:08 rms-change max change #iterations 8.668959 295.7666 at 10iterations 4.982074 137.8094 at 20iterations 2.840804 72.10844 at 30iterations 1.611424 44.16128 at 40iterations 0.9051039 20.37603 at 50iterations 0.5105783 12.00959 at 60iterations 0.2864562 7.317593 at 70iterations 0.1603611 3.514973 at 80iterations 8.9691311E-02 2.120720 at 90iterations 4.9991090E-02 1.304407 at 100iterations 2.7928295E-02 0.6191700 at 110iterations 1.5562396E-02 0.3296599 at 120iterations 8.7057324E-03 0.2069149 at 130iterations 4.8396010E-03 0.1174155 at 140iterations 2.6965321E-03 6.0185671E-02 at 150iterations 1.5024020E-03 3.1203508E-02 at 160iterations 8.3648303E-04 1.7017365E-02 at 170iterations 4.6657288E-04 1.0939121E-02 at 180iterations finished qdiffx linear iterations at : 09:48:19 total time elapsed so far: 13.13000 # loops : 180 mean,max change (kT/e) : 4.6657288E-04 1.0939121E-02 energy calculations done at 13.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 09:48:20 13.335u 0.258s 0:13.95 97.3% 0+0k 0+0io 0pf+0w