Sun Oct 9 13:22:31 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 13:22:31 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7022804 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): 22.09900 72.79100 ymin,ymax (A): -14.29200 36.11400 zmin,zma (A): 1.895000 45.07700 x,y,z range (A): 50.69200 50.40600 43.18200 scale (grids/A): 0.7022804 object centre (A): 47.44500 10.91100 23.48600 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.28835 91.48566 90.77526 assigned negative charge : -360.0896 centred at (gu) : 89.29684 91.64474 90.83916 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7824 nv = 96 ne = 84 npr = 47653 no. pairs analyzed = 47653 no. exposed pairs = 2979 no. arc points = 20730 no. surface atoms = 1004 nbur = 1362 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 492 mr = 4332 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1893 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8825 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1457693E-08 -5.9574115E-09 midg,1,midg; midg,igrid,midg 7.9929926E-08 -7.3850771E-08 1,midg,midg; igrid,midg,midg 3.6692654E-08 2.0488336E-08 gauss-seidel spectral radius is 0.9894625 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 13:22:31 rms-change max change #iterations 0.2097709 27.43212 at 10iterations 2.5819201E-02 3.187077 at 20iterations 3.6613476E-03 0.5027618 at 30iterations 8.0937048E-04 0.1136322 at 40iterations 2.5832729E-04 3.8688660E-02 at 50iterations finished qdiffx linear iterations at : 13:22:34 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.5832729E-04 3.8688660E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 13:22:35 3.341u 0.179s 0:03.79 92.6% 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 13:22:35 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.106841 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): 22.09900 72.79100 ymin,ymax (A): -14.29200 36.11400 zmin,zma (A): 1.895000 45.07700 x,y,z range (A): 50.69200 50.40600 43.18200 scale (grids/A): 2.106841 object centre (A): 47.44500 10.91100 23.48600 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 87.86446 94.45670 92.32545 assigned negative charge : -360.0896 centred at (gu) : 87.89046 94.93405 92.51726 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 83297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20730 grid for indexing accessible points = 1.400000 m= 32989 mr = 58130 m= 6048 mr = 24475 m= 541 mr = 3929 m= 8 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.4200000 number of dielectric boundary points 36063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17649 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) : 0.7022804 object centre at (A) : 47.44500 10.91100 23.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4511150E-02 1.2660881E-02 midg,1,midg; midg,igrid,midg 8.3842278E-03 -6.2435545E-02 1,midg,midg; igrid,midg,midg 4.1811369E-02 -8.7530548E-03 gauss-seidel spectral radius is 0.9988486 estimated iterations to convergence 233 setup time was (sec) 0.6400000 now iterating at: 13:22:35 rms-change max change #iterations 4.998834 236.9726 at 10iterations 2.477321 86.61130 at 20iterations 1.233526 37.36298 at 30iterations 0.6130930 18.00207 at 40iterations 0.3068533 8.577865 at 50iterations 0.1532009 5.117378 at 60iterations 7.6394096E-02 2.605774 at 70iterations 3.8176745E-02 1.163174 at 80iterations 1.9291079E-02 0.6419172 at 90iterations 9.8271146E-03 0.2816534 at 100iterations 5.0774999E-03 0.1517963 at 110iterations 2.7408653E-03 8.1237793E-02 at 120iterations finished qdiffx linear iterations at : 13:22:43 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.7408653E-03 8.1237793E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 13:22:43 7.895u 0.180s 0:08.57 94.1% 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 13:22:43 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.160262 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): 22.09900 72.79100 ymin,ymax (A): -14.29200 36.11400 zmin,zma (A): 1.895000 45.07700 x,y,z range (A): 50.69200 50.40600 43.18200 scale (grids/A): 3.160262 object centre (A): 47.44500 10.91100 23.48600 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 86.79671 96.68491 93.48808 assigned negative charge : -360.0896 centred at (gu) : 86.83561 97.40102 93.77579 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 192077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20730 grid for indexing accessible points = 1.400000 m= 102414 mr = 140148 m= 41076 mr = 84063 m= 11513 mr = 33490 m= 2226 mr = 8755 m= 282 mr = 1666 m= 9 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1238 time to turn everything in is 1.260000 number of dielectric boundary points 81277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17796 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) : 2.106841 object centre at (A) : 47.44500 10.91100 23.48600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6261237 -2.9993873E-02 midg,1,midg; midg,igrid,midg 0.2046335 -0.5558760 1,midg,midg; igrid,midg,midg 0.3519266 -0.3829610 gauss-seidel spectral radius is 0.9993035 estimated iterations to convergence 299 setup time was (sec) 1.500000 now iterating at: 13:22:45 rms-change max change #iterations 11.22374 323.7668 at 10iterations 6.698463 142.6969 at 20iterations 3.975610 75.69735 at 30iterations 2.357894 44.32227 at 40iterations 1.395243 23.36900 at 50iterations 0.8237881 16.04416 at 60iterations 0.4844574 8.127075 at 70iterations 0.2857910 4.940603 at 80iterations 0.1674830 2.907441 at 90iterations 9.8802134E-02 1.676178 at 100iterations 5.8231711E-02 0.9517441 at 110iterations 3.4474444E-02 0.5552063 at 120iterations 2.0649064E-02 0.3661957 at 130iterations 1.2596072E-02 0.2451191 at 140iterations 7.9819532E-03 0.1742058 at 150iterations 5.3131129E-03 0.1081238 at 160iterations 3.7791552E-03 8.2733154E-02 at 170iterations 2.8631210E-03 6.0150146E-02 at 180iterations finished qdiffx linear iterations at : 13:22:56 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 2.8631210E-03 6.0150146E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 13:22:57 13.110u 0.221s 0:13.65 97.6% 0+0k 0+0io 0pf+0w