Tue Oct 11 06:28:33 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 Tue Oct 11 2011 at 06:28:33 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 # of charge parameter records: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1439 !!! WARNING: ASL 34 has a net charge of -0.1000 !!! WARNING: GLM 64 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: 0.7652293 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): 0.4970001 46.42700 ymin,ymax (A): -24.71200 21.81000 zmin,zma (A): 64.99000 100.0190 x,y,z range (A): 45.93000 46.52200 35.02901 scale (grids/A): 0.7652293 object centre (A): 23.46200 -1.451000 82.50450 number of atom coordinates read : 1439 total number of charged atoms : 1352 net assigned charge : 0.3060050 assigned positive charge : 216.0405 centred at (gu) : 91.20724 88.13610 89.19714 assigned negative charge : -215.7343 centred at (gu) : 91.03902 88.02383 89.13412 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6134 nv = 96 ne = 84 npr = 27822 no. pairs analyzed = 27822 no. exposed pairs = 1804 no. arc points = 12869 no. surface atoms = 622 nbur = 817 mkacc time = 5.9999987E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 3544 m= 6 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2300000 number of dielectric boundary points 2962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 968 ## 77 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6119 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0911263E-08 6.9270875E-08 midg,1,midg; midg,igrid,midg -1.6662703E-07 9.5618581E-08 1,midg,midg; igrid,midg,midg -1.4489224E-07 2.4522856E-07 gauss-seidel spectral radius is 0.9910293 estimated iterations to convergence 86 setup time was (sec) 0.4400000 now iterating at: 06:28:34 rms-change max change #iterations 0.2341375 33.09886 at 10iterations 3.3605278E-02 4.409849 at 20iterations 4.8850430E-03 0.6216774 at 30iterations 7.2038593E-04 9.6343994E-02 at 40iterations 1.2262544E-04 2.0553589E-02 at 50iterations finished qdiffx linear iterations at : 06:28:36 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.2262544E-04 2.0553589E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 06:28:37 3.283u 0.155s 0:04.14 82.8% 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 Tue Oct 11 2011 at 06:28:37 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1439 !!! WARNING: ASL 34 has a net charge of -0.1000 !!! WARNING: GLM 64 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.295688 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): 0.4970001 46.42700 ymin,ymax (A): -24.71200 21.81000 zmin,zma (A): 64.99000 100.0190 x,y,z range (A): 45.93000 46.52200 35.02901 scale (grids/A): 2.295688 object centre (A): 23.46200 -1.451000 82.50450 number of atom coordinates read : 1439 total number of charged atoms : 1352 net assigned charge : 0.3060050 assigned positive charge : 216.0405 centred at (gu) : 93.62233 84.40864 87.59164 assigned negative charge : -215.7343 centred at (gu) : 93.11721 84.07185 87.40262 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 63869 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12869 grid for indexing accessible points = 1.400000 m= 27804 mr = 44993 m= 6432 mr = 21719 m= 683 mr = 4566 m= 29 mr = 357 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1450 time to turn everything in is 0.5100000 number of dielectric boundary points 27179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10787 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) : 0.7652293 object centre at (A) : 23.46200 -1.451000 82.50450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5657354E-03 1.0766430E-02 midg,1,midg; midg,igrid,midg -9.9724546E-02 1.5769185E-02 1,midg,midg; igrid,midg,midg 8.0499817E-03 3.4215439E-02 gauss-seidel spectral radius is 0.9989229 estimated iterations to convergence 241 setup time was (sec) 0.8000000 now iterating at: 06:28:38 rms-change max change #iterations 4.339327 179.3403 at 10iterations 2.222123 90.07083 at 20iterations 1.132447 36.04289 at 30iterations 0.5776819 18.41391 at 40iterations 0.2958040 9.788329 at 50iterations 0.1502480 4.911730 at 60iterations 7.6673776E-02 2.691605 at 70iterations 3.9073680E-02 1.292671 at 80iterations 1.9990534E-02 0.6256976 at 90iterations 1.0259944E-02 0.3595836 at 100iterations 5.2422644E-03 0.1711050 at 110iterations 2.6901532E-03 9.0070724E-02 at 120iterations finished qdiffx linear iterations at : 06:28:45 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 2.6901532E-03 9.0070724E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 06:28:46 7.506u 0.200s 0:08.46 91.0% 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 Tue Oct 11 2011 at 06:28:46 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1439 !!! WARNING: ASL 34 has a net charge of -0.1000 !!! WARNING: GLM 64 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.443532 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): 0.4970001 46.42700 ymin,ymax (A): -24.71200 21.81000 zmin,zma (A): 64.99000 100.0190 x,y,z range (A): 45.93000 46.52200 35.02901 scale (grids/A): 3.443532 object centre (A): 23.46200 -1.451000 82.50450 number of atom coordinates read : 1439 total number of charged atoms : 1352 net assigned charge : 0.3060050 assigned positive charge : 216.0405 centred at (gu) : 95.43359 81.61302 86.38766 assigned negative charge : -215.7343 centred at (gu) : 94.67592 81.10789 86.10395 start vw surface at 0.1200000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 146696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12869 grid for indexing accessible points = 1.400000 m= 83048 mr = 107584 m= 38186 mr = 70149 m= 12487 mr = 32214 m= 2793 mr = 10015 m= 405 mr = 2032 m= 18 mr = 295 m= 0 mr = 2 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 4834 time to turn everything in is 1.510000 number of dielectric boundary points 61342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 10816 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) : 2.295688 object centre at (A) : 23.46200 -1.451000 82.50450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9867205E-02 5.9559856E-02 midg,1,midg; midg,igrid,midg -1.526184 0.1483320 1,midg,midg; igrid,midg,midg 1.5355637E-02 0.1846313 gauss-seidel spectral radius is 0.9993145 estimated iterations to convergence 301 setup time was (sec) 1.780000 now iterating at: 06:28:48 rms-change max change #iterations 9.363043 335.4294 at 10iterations 5.594740 127.4781 at 20iterations 3.329486 74.21265 at 30iterations 1.973109 47.81673 at 40iterations 1.166294 24.72130 at 50iterations 0.6886190 13.49172 at 60iterations 0.4072983 8.080851 at 70iterations 0.2409339 4.840219 at 80iterations 0.1418298 2.628881 at 90iterations 8.3513148E-02 1.572353 at 100iterations 4.9263831E-02 0.9325256 at 110iterations 2.8988998E-02 0.5451584 at 120iterations 1.7155079E-02 0.3075123 at 130iterations 1.0163659E-02 0.1808634 at 140iterations 6.0586426E-03 0.1190948 at 150iterations 3.6612416E-03 7.1685791E-02 at 160iterations 2.2802535E-03 5.1918030E-02 at 170iterations 1.4809716E-03 3.3031464E-02 at 180iterations finished qdiffx linear iterations at : 06:28:57 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 1.4809716E-03 3.3031464E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.62000 DelPhi exited at 06:28:58 11.624u 0.269s 0:12.40 95.8% 0+0k 0+0io 0pf+0w