Sun Oct 9 13:24:54 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 Sun Oct 9 2011 at 13:24:54 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6751631 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): -7.269000 44.32200 ymin,ymax (A): -13.90200 38.82600 zmin,zma (A): 1.511000 44.92200 x,y,z range (A): 51.59100 52.72800 43.41100 scale (grids/A): 0.6751631 object centre (A): 18.52650 12.46200 23.21650 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500024 assigned positive charge : 365.4110 centred at (gu) : 89.92609 90.62734 90.65942 assigned negative charge : -361.9116 centred at (gu) : 89.90409 90.80792 90.73199 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7327 nv = 96 ne = 84 npr = 48128 no. pairs analyzed = 48128 no. exposed pairs = 2998 no. arc points = 21132 no. surface atoms = 1002 nbur = 1391 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4042 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2035 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8437 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9089794E-08 -6.8675736E-09 midg,1,midg; midg,igrid,midg 5.4182031E-08 -4.0902556E-08 1,midg,midg; igrid,midg,midg 7.9991258E-09 1.9460197E-08 gauss-seidel spectral radius is 0.9886069 estimated iterations to convergence 76 setup time was (sec) 0.4800000 now iterating at: 13:24:55 rms-change max change #iterations 0.1766896 25.92743 at 10iterations 1.9622887E-02 3.116207 at 20iterations 2.3704304E-03 0.4046097 at 30iterations 3.6972121E-04 4.9160004E-02 at 40iterations 8.5983571E-05 1.2344360E-02 at 50iterations finished qdiffx linear iterations at : 13:24:57 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 8.5983571E-05 1.2344360E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 13:24:58 3.106u 0.154s 0:03.56 91.2% 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 13:24:58 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.025489 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): -7.269000 44.32200 ymin,ymax (A): -13.90200 38.82600 zmin,zma (A): 1.511000 44.92200 x,y,z range (A): 51.59100 52.72800 43.41100 scale (grids/A): 2.025489 object centre (A): 18.52650 12.46200 23.21650 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500024 assigned positive charge : 365.4110 centred at (gu) : 89.77766 91.88168 91.97787 assigned negative charge : -361.9116 centred at (gu) : 89.71214 92.42371 92.19570 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21132 grid for indexing accessible points = 1.400000 m= 29323 mr = 53760 m= 4990 mr = 21775 m= 450 mr = 3113 m= 9 mr = 253 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 0.5600000 number of dielectric boundary points 33638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17814 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) : 0.6751631 object centre at (A) : 18.52650 12.46200 23.21650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7841907E-02 4.8663705E-03 midg,1,midg; midg,igrid,midg 1.5654625E-02 -6.1561834E-02 1,midg,midg; igrid,midg,midg 3.5419956E-02 4.1789939E-03 gauss-seidel spectral radius is 0.9987694 estimated iterations to convergence 226 setup time was (sec) 0.8100000 now iterating at: 13:24:59 rms-change max change #iterations 4.614019 206.6980 at 10iterations 2.230393 72.02688 at 20iterations 1.086984 36.69735 at 30iterations 0.5289347 15.28374 at 40iterations 0.2578801 8.508135 at 50iterations 0.1252811 3.771881 at 60iterations 6.1109014E-02 1.835861 at 70iterations 2.9687235E-02 0.9343433 at 80iterations 1.4543250E-02 0.4145756 at 90iterations 7.1219467E-03 0.2204170 at 100iterations 3.5013668E-03 0.1138706 at 110iterations 1.7314508E-03 5.8018863E-02 at 120iterations finished qdiffx linear iterations at : 13:25:04 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 1.7314508E-03 5.8018863E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 13:25:05 6.953u 0.152s 0:07.43 95.5% 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 13:25:05 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 = 2393 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: 3.038234 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): -7.269000 44.32200 ymin,ymax (A): -13.90200 38.82600 zmin,zma (A): 1.511000 44.92200 x,y,z range (A): 51.59100 52.72800 43.41100 scale (grids/A): 3.038234 object centre (A): 18.52650 12.46200 23.21650 number of atom coordinates read : 2393 total number of charged atoms : 2251 net assigned charge : 3.500024 assigned positive charge : 365.4110 centred at (gu) : 89.66650 92.82213 92.96659 assigned negative charge : -361.9116 centred at (gu) : 89.56809 93.63541 93.29359 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 179241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21132 grid for indexing accessible points = 1.400000 m= 93172 mr = 129971 m= 35274 mr = 76323 m= 9098 mr = 28392 m= 1817 mr = 6849 m= 218 mr = 1366 m= 3 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 75801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 18008 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) : 2.025489 object centre at (A) : 18.52650 12.46200 23.21650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4816197 -5.7067100E-02 midg,1,midg; midg,igrid,midg 0.2986796 -0.7284475 1,midg,midg; igrid,midg,midg 0.3420616 -0.1971532 gauss-seidel spectral radius is 0.9992844 estimated iterations to convergence 295 setup time was (sec) 1.700000 now iterating at: 13:25:07 rms-change max change #iterations 10.58763 397.7382 at 10iterations 6.232417 145.9715 at 20iterations 3.670718 82.19938 at 30iterations 2.160159 38.88474 at 40iterations 1.267232 24.43648 at 50iterations 0.7388497 13.81489 at 60iterations 0.4323021 8.522030 at 70iterations 0.2522848 4.552780 at 80iterations 0.1467666 2.496292 at 90iterations 8.5572712E-02 1.651203 at 100iterations 4.9908731E-02 0.9763575 at 110iterations 2.9094275E-02 0.5159869 at 120iterations 1.6949205E-02 0.2903442 at 130iterations 9.9174120E-03 0.1662827 at 140iterations 5.8303578E-03 0.1006355 at 150iterations 3.4610957E-03 6.3735962E-02 at 160iterations 2.0978597E-03 4.0172577E-02 at 170iterations 1.3032190E-03 2.7500153E-02 at 180iterations finished qdiffx linear iterations at : 13:25:17 total time elapsed so far: 11.44000 # loops : 180 mean,max change (kT/e) : 1.3032190E-03 2.7500153E-02 energy calculations done at 11.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 13:25:17 11.653u 0.167s 0:12.12 97.4% 0+0k 0+0io 0pf+0w