Sat Oct 8 15:52:12 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 Sat Oct 8 2011 at 15:52:12 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 = 2363 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: 0.5937291 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): -1.831000 45.78500 ymin,ymax (A): -15.68500 29.83000 zmin,zma (A): -17.25900 42.70100 x,y,z range (A): 47.61600 45.51500 59.96000 scale (grids/A): 0.5937291 object centre (A): 21.97700 7.072500 12.72100 number of atom coordinates read : 2363 total number of charged atoms : 2283 net assigned charge : 3.000001 assigned positive charge : 351.4151 centred at (gu) : 90.46543 88.64880 88.53264 assigned negative charge : -348.4157 centred at (gu) : 90.45925 88.76578 88.58953 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5399 nv = 96 ne = 84 npr = 48163 no. pairs analyzed = 48163 no. exposed pairs = 2932 no. arc points = 20323 no. surface atoms = 1014 nbur = 1349 mkacc time = 0.1300000 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 = 1.456000 m= 273 mr = 2909 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3100000 number of dielectric boundary points 2736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2114 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6968 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4852956E-09 -3.9015818E-10 midg,1,midg; midg,igrid,midg 5.5614757E-09 -1.6036793E-09 1,midg,midg; igrid,midg,midg 7.2634426E-10 1.2594911E-09 gauss-seidel spectral radius is 0.9852988 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 15:52:12 rms-change max change #iterations 9.5592432E-02 16.25239 at 10iterations 7.9931673E-03 1.218254 at 20iterations 6.9320161E-04 0.1091919 at 30iterations 8.5035528E-05 1.4742851E-02 at 40iterations 1.7234996E-05 3.4658909E-03 at 50iterations finished qdiffx linear iterations at : 15:52:16 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 1.7234996E-05 3.4658909E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 15:52:16 4.054u 0.266s 0:04.77 90.3% 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 Sat Oct 8 2011 at 15:52:16 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 = 2363 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: 1.781188 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): -1.831000 45.78500 ymin,ymax (A): -15.68500 29.83000 zmin,zma (A): -17.25900 42.70100 x,y,z range (A): 47.61600 45.51500 59.96000 scale (grids/A): 1.781188 object centre (A): 21.97700 7.072500 12.72100 number of atom coordinates read : 2363 total number of charged atoms : 2283 net assigned charge : 3.000001 assigned positive charge : 351.4151 centred at (gu) : 91.39574 85.94565 85.59750 assigned negative charge : -348.4157 centred at (gu) : 91.37780 86.29706 85.76828 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 59869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20323 grid for indexing accessible points = 1.400000 m= 19731 mr = 41294 m= 2669 mr = 14001 m= 114 mr = 1551 m= 0 mr = 26 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 465 time to turn everything in is 0.5300000 number of dielectric boundary points 25511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17794 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) : 0.5937291 object centre at (A) : 21.97700 7.072500 12.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5141574E-02 1.4019042E-02 midg,1,midg; midg,igrid,midg 1.3586755E-02 -3.2164077E-03 1,midg,midg; igrid,midg,midg -9.9789130E-04 -1.5869349E-02 gauss-seidel spectral radius is 0.9984127 estimated iterations to convergence 199 setup time was (sec) 0.8300000 now iterating at: 15:52:18 rms-change max change #iterations 3.468002 159.8262 at 10iterations 1.540259 53.94305 at 20iterations 0.6771108 24.70698 at 30iterations 0.2993100 10.62482 at 40iterations 0.1325044 4.573608 at 50iterations 5.8571260E-02 1.962714 at 60iterations 2.5925124E-02 0.9400820 at 70iterations 1.1518858E-02 0.4657731 at 80iterations 5.0968044E-03 0.1721106 at 90iterations 2.2484802E-03 8.6486101E-02 at 100iterations 9.9811889E-04 3.9608955E-02 at 110iterations 4.4169716E-04 1.7300606E-02 at 120iterations finished qdiffx linear iterations at : 15:52:26 total time elapsed so far: 9.100000 # loops : 120 mean,max change (kT/e) : 4.4169716E-04 1.7300606E-02 energy calculations done at 9.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 15:52:26 9.277u 0.311s 0:09.84 97.3% 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 Sat Oct 8 2011 at 15:52:26 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 = 2363 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: 2.671781 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): -1.831000 45.78500 ymin,ymax (A): -15.68500 29.83000 zmin,zma (A): -17.25900 42.70100 x,y,z range (A): 47.61600 45.51500 59.96000 scale (grids/A): 2.671781 object centre (A): 21.97700 7.072500 12.72100 number of atom coordinates read : 2363 total number of charged atoms : 2283 net assigned charge : 3.000001 assigned positive charge : 351.4151 centred at (gu) : 92.09338 83.91853 83.39612 assigned negative charge : -348.4157 centred at (gu) : 92.06671 84.44551 83.65248 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 139146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20323 grid for indexing accessible points = 1.400000 m= 65783 mr = 100841 m= 21421 mr = 52824 m= 4572 mr = 16720 m= 476 mr = 3266 m= 15 mr = 287 m= 0 mr = 2 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 1541 time to turn everything in is 1.350000 number of dielectric boundary points 57473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 18256 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) : 1.781188 object centre at (A) : 21.97700 7.072500 12.72100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3289127 0.4347867 midg,1,midg; midg,igrid,midg 0.1561590 -4.6927970E-02 1,midg,midg; igrid,midg,midg -2.4655249E-03 -0.2721718 gauss-seidel spectral radius is 0.9991928 estimated iterations to convergence 278 setup time was (sec) 1.660000 now iterating at: 15:52:28 rms-change max change #iterations 8.554093 308.1204 at 10iterations 4.930220 121.4600 at 20iterations 2.819716 74.54540 at 30iterations 1.600836 34.66456 at 40iterations 0.9083741 19.38280 at 50iterations 0.5142682 11.56720 at 60iterations 0.2913547 6.492752 at 70iterations 0.1642141 3.277812 at 80iterations 9.2690222E-02 1.876644 at 90iterations 5.2079562E-02 1.109880 at 100iterations 2.9347032E-02 0.5871201 at 110iterations 1.6491029E-02 0.3366899 at 120iterations 9.2655933E-03 0.1985027 at 130iterations 5.2097314E-03 0.1162291 at 140iterations 2.9285096E-03 5.8683395E-02 at 150iterations 1.6487429E-03 3.4269333E-02 at 160iterations 9.3197147E-04 2.0234108E-02 at 170iterations 5.2900496E-04 1.1191368E-02 at 180iterations finished qdiffx linear iterations at : 15:52:41 total time elapsed so far: 14.93000 # loops : 180 mean,max change (kT/e) : 5.2900496E-04 1.1191368E-02 energy calculations done at 14.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.11000 DelPhi exited at 15:52:42 15.110u 0.306s 0:15.77 97.7% 0+0k 0+0io 0pf+0w