Mon Oct 10 16:21:55 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 16:21:55 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 = 4735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5497561 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): -62.76200 -7.531000 ymin,ymax (A): -29.75900 34.73300 zmin,zma (A): -35.49700 29.25900 x,y,z range (A): 55.23100 64.49200 64.75600 scale (grids/A): 0.5497561 object centre (A): -35.14650 2.487001 -3.119001 number of atom coordinates read : 4735 total number of charged atoms : 4577 net assigned charge : 7.000029 assigned positive charge : 713.1519 centred at (gu) : 90.41295 90.11324 91.53447 assigned negative charge : -706.1561 centred at (gu) : 90.42046 90.06310 91.52425 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9197 nv = 96 ne = 84 npr = 97469 no. pairs analyzed = 97469 no. exposed pairs = 5708 no. arc points = 38421 no. surface atoms = 1926 nbur = 2809 mkacc time = 0.2500000 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 = 1.568000 m= 379 mr = 5123 m= 0 mr = 17 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4800000 number of dielectric boundary points 4436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3942 ## 508 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12126 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6382291E-10 9.0677815E-10 midg,1,midg; midg,igrid,midg -1.0659188E-10 1.1355370E-09 1,midg,midg; igrid,midg,midg 5.3600580E-10 4.5187709E-10 gauss-seidel spectral radius is 0.9830642 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 16:21:56 rms-change max change #iterations 9.7386017E-02 12.36087 at 10iterations 7.2251903E-03 0.9156036 at 20iterations 1.1018583E-03 0.2022591 at 30iterations 4.0321233E-04 6.5734863E-02 at 40iterations 1.7141884E-04 2.3349762E-02 at 50iterations finished qdiffx linear iterations at : 16:22:00 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 1.7141884E-04 2.3349762E-02 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.660000 DelPhi exited at 16:22:00 4.662u 0.414s 0:05.60 90.5% 0+0k 0+0io 4pf+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 16:22:01 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 = 4735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.649268 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): -62.76200 -7.531000 ymin,ymax (A): -29.75900 34.73300 zmin,zma (A): -35.49700 29.25900 x,y,z range (A): 55.23100 64.49200 64.75600 scale (grids/A): 1.649268 object centre (A): -35.14650 2.487001 -3.119001 number of atom coordinates read : 4735 total number of charged atoms : 4577 net assigned charge : 7.000029 assigned positive charge : 713.1519 centred at (gu) : 91.23721 90.33847 94.60175 assigned negative charge : -706.1561 centred at (gu) : 91.26100 90.18885 94.57247 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38421 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32994 mr = 73583 m= 3452 mr = 22993 m= 108 mr = 1726 m= 0 mr = 8 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.8300000 number of dielectric boundary points 41197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 405 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 35115 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) : 0.5497561 object centre at (A) : -35.14650 2.487001 -3.119001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2051657E-03 1.7065195E-02 midg,1,midg; midg,igrid,midg 1.7087735E-02 1.6097903E-02 1,midg,midg; igrid,midg,midg 5.5304584E-03 3.9334390E-03 gauss-seidel spectral radius is 0.9983891 estimated iterations to convergence 198 setup time was (sec) 1.200000 now iterating at: 16:22:02 rms-change max change #iterations 4.403015 204.3866 at 10iterations 1.933870 62.97305 at 20iterations 0.8477206 25.06152 at 30iterations 0.3725388 11.87119 at 40iterations 0.1636681 4.884062 at 50iterations 7.1881816E-02 2.133246 at 60iterations 3.1808745E-02 0.9639530 at 70iterations 1.4099648E-02 0.4337730 at 80iterations 6.3149179E-03 0.1862183 at 90iterations 2.9376084E-03 9.4268799E-02 at 100iterations 1.4474308E-03 4.7279358E-02 at 110iterations 8.0650114E-04 2.3157120E-02 at 120iterations finished qdiffx linear iterations at : 16:22:12 total time elapsed so far: 10.91000 # loops : 120 mean,max change (kT/e) : 8.0650114E-04 2.3157120E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 16:22:12 11.076u 0.453s 0:11.80 97.6% 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 Mon Oct 10 2011 at 16:22:12 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 = 4735 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.473902 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): -62.76200 -7.531000 ymin,ymax (A): -29.75900 34.73300 zmin,zma (A): -35.49700 29.25900 x,y,z range (A): 55.23100 64.49200 64.75600 scale (grids/A): 2.473902 object centre (A): -35.14650 2.487001 -3.119001 number of atom coordinates read : 4735 total number of charged atoms : 4577 net assigned charge : 7.000029 assigned positive charge : 713.1519 centred at (gu) : 91.85549 90.50732 96.90216 assigned negative charge : -706.1561 centred at (gu) : 91.89134 90.28320 96.85863 start vw surface at 0.1700000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 239680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38421 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 114012 mr = 179659 m= 32758 mr = 91363 m= 5444 mr = 24563 m= 443 mr = 3602 m= 9 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 2088 time to turn everything in is 2.090000 number of dielectric boundary points 92927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 36573 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) : 1.649268 object centre at (A) : -35.14650 2.487001 -3.119001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7126745E-02 0.4672348 midg,1,midg; midg,igrid,midg 0.3623526 0.1682224 1,midg,midg; igrid,midg,midg 0.1042618 8.2694434E-02 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 2.450000 now iterating at: 16:22:15 rms-change max change #iterations 11.37021 413.6378 at 10iterations 6.686622 173.8367 at 20iterations 3.904070 81.51286 at 30iterations 2.275301 45.44880 at 40iterations 1.316602 25.01047 at 50iterations 0.7612255 15.13156 at 60iterations 0.4384496 7.931978 at 70iterations 0.2522928 4.935921 at 80iterations 0.1449277 2.385011 at 90iterations 8.3159439E-02 1.428848 at 100iterations 4.7660887E-02 0.7838514 at 110iterations 2.7283808E-02 0.4787235 at 120iterations 1.5628619E-02 0.2545195 at 130iterations 8.9599192E-03 0.1588974 at 140iterations 5.1329592E-03 8.9884758E-02 at 150iterations 2.9620396E-03 5.0913930E-02 at 160iterations 1.7172764E-03 2.9090881E-02 at 170iterations 1.0156786E-03 1.8845558E-02 at 180iterations finished qdiffx linear iterations at : 16:22:32 total time elapsed so far: 19.22000 # loops : 180 mean,max change (kT/e) : 1.0156786E-03 1.8845558E-02 energy calculations done at 19.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.39000 DelPhi exited at 16:22:33 19.397u 0.501s 0:20.17 98.6% 0+0k 0+0io 0pf+0w