Tue Oct 11 05:17:08 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 Tue Oct 11 2011 at 05:17:09 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2243 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN7 739 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6913561 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): 19.71900 63.10400 ymin,ymax (A): -3.539000 33.55700 zmin,zma (A): 20.28900 71.78201 x,y,z range (A): 43.38500 37.09600 51.49300 scale (grids/A): 0.6913561 object centre (A): 41.41150 15.00900 46.03550 number of atom coordinates read : 2243 total number of charged atoms : 1938 net assigned charge : 8.600008 assigned positive charge : 314.2170 centred at (gu) : 90.18645 89.68163 89.36164 assigned negative charge : -305.6172 centred at (gu) : 90.34918 89.68076 89.32171 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6743 nv = 96 ne = 84 npr = 40847 no. pairs analyzed = 40847 no. exposed pairs = 2514 no. arc points = 17050 no. surface atoms = 864 nbur = 1379 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3855 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3232 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0585238E-08 5.5474789E-08 midg,1,midg; midg,igrid,midg 5.2251877E-08 4.6786056E-08 1,midg,midg; igrid,midg,midg 9.9401440E-08 -6.4195986E-09 gauss-seidel spectral radius is 0.9890965 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 05:17:09 rms-change max change #iterations 0.1759949 24.32758 at 10iterations 2.1071106E-02 2.814430 at 20iterations 2.4739460E-03 0.3262758 at 30iterations 3.2042761E-04 4.7164917E-02 at 40iterations 5.3482108E-05 6.9198608E-03 at 50iterations finished qdiffx linear iterations at : 05:17:12 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.3482108E-05 6.9198608E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 05:17:13 3.400u 0.224s 0:04.19 86.3% 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 Tue Oct 11 2011 at 05:17:13 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2243 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN7 739 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.074068 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): 19.71900 63.10400 ymin,ymax (A): -3.539000 33.55700 zmin,zma (A): 20.28900 71.78201 x,y,z range (A): 43.38500 37.09600 51.49300 scale (grids/A): 2.074068 object centre (A): 41.41150 15.00900 46.03550 number of atom coordinates read : 2243 total number of charged atoms : 1938 net assigned charge : 8.600008 assigned positive charge : 314.2170 centred at (gu) : 90.55933 89.04501 88.08461 assigned negative charge : -305.6172 centred at (gu) : 91.04749 89.04236 87.96525 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71307 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17050 grid for indexing accessible points = 1.400000 m= 28711 mr = 50561 m= 5322 mr = 21749 m= 410 mr = 3532 m= 6 mr = 189 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 15377 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) : 0.6913561 object centre at (A) : 41.41150 15.00900 46.03550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9629673E-02 4.9401134E-02 midg,1,midg; midg,igrid,midg 2.3490489E-02 2.2459248E-02 1,midg,midg; igrid,midg,midg 4.0781450E-02 1.3316653E-02 gauss-seidel spectral radius is 0.9987803 estimated iterations to convergence 227 setup time was (sec) 0.8000000 now iterating at: 05:17:14 rms-change max change #iterations 4.419831 203.7114 at 10iterations 2.164824 78.40665 at 20iterations 1.052648 33.27481 at 30iterations 0.5169786 17.59005 at 40iterations 0.2522537 8.349588 at 50iterations 0.1235069 4.451503 at 60iterations 6.0514692E-02 1.840097 at 70iterations 2.9608252E-02 0.8681355 at 80iterations 1.4424365E-02 0.4407959 at 90iterations 7.0911809E-03 0.2157726 at 100iterations 3.4748246E-03 0.1105061 at 110iterations 1.7122462E-03 4.8974991E-02 at 120iterations finished qdiffx linear iterations at : 05:17:20 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.7122462E-03 4.8974991E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 05:17:21 7.562u 0.244s 0:08.47 92.0% 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 05:17:21 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2243 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: ZN7 739 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 3.111102 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): 19.71900 63.10400 ymin,ymax (A): -3.539000 33.55700 zmin,zma (A): 20.28900 71.78201 x,y,z range (A): 43.38500 37.09600 51.49300 scale (grids/A): 3.111102 object centre (A): 41.41150 15.00900 46.03550 number of atom coordinates read : 2243 total number of charged atoms : 1938 net assigned charge : 8.600008 assigned positive charge : 314.2170 centred at (gu) : 90.83894 88.56741 87.12696 assigned negative charge : -305.6172 centred at (gu) : 91.57133 88.56351 86.94784 start vw surface at 0.1800000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 164508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17050 grid for indexing accessible points = 1.400000 m= 89727 mr = 121975 m= 36158 mr = 74624 m= 10011 mr = 29631 m= 1836 mr = 7681 m= 154 mr = 1345 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.670000 number of dielectric boundary points 67057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 15504 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) : 2.074068 object centre at (A) : 41.41150 15.00900 46.03550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3841321 0.3775095 midg,1,midg; midg,igrid,midg 0.2059938 0.2005979 1,midg,midg; igrid,midg,midg 0.3333964 0.2909668 gauss-seidel spectral radius is 0.9992820 estimated iterations to convergence 294 setup time was (sec) 1.990000 now iterating at: 05:17:24 rms-change max change #iterations 9.905250 331.6106 at 10iterations 5.857406 155.5403 at 20iterations 3.451517 73.87911 at 30iterations 2.024065 41.73297 at 40iterations 1.186810 25.41232 at 50iterations 0.6945555 16.50997 at 60iterations 0.4055227 8.063709 at 70iterations 0.2370844 4.980759 at 80iterations 0.1383202 2.588868 at 90iterations 8.0500044E-02 1.657972 at 100iterations 4.6972688E-02 0.8947807 at 110iterations 2.7403761E-02 0.5366961 at 120iterations 1.6005613E-02 0.2886887 at 130iterations 9.3953293E-03 0.1747818 at 140iterations 5.5731852E-03 0.1055145 at 150iterations 3.3384084E-03 6.2452793E-02 at 160iterations 2.0663631E-03 4.1168213E-02 at 170iterations 1.3315924E-03 2.9139519E-02 at 180iterations finished qdiffx linear iterations at : 05:17:33 total time elapsed so far: 11.46000 # loops : 180 mean,max change (kT/e) : 1.3315924E-03 2.9139519E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.66000 DelPhi exited at 05:17:34 11.661u 0.205s 0:12.29 96.5% 0+0k 0+0io 0pf+0w