Sat Oct 15 13:20:59 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 Sat Oct 15 2011 at 13:20:59 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 0.6296873 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): -12.36600 37.15300 ymin,ymax (A): -22.25000 34.28600 zmin,zma (A): -12.19900 40.80300 x,y,z range (A): 49.51900 56.53600 53.00200 scale (grids/A): 0.6296873 object centre (A): 12.39350 6.018000 14.30200 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.5399 centred at (gu) : 90.75719 89.39412 90.17514 assigned negative charge : -386.0156 centred at (gu) : 90.71851 89.35526 90.17547 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6624 nv = 96 ne = 84 npr = 52613 no. pairs analyzed = 52613 no. exposed pairs = 3094 no. arc points = 22102 no. surface atoms = 1054 nbur = 1522 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3531 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3400000 number of dielectric boundary points 3374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2225 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8206 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7202890E-09 5.0207394E-09 midg,1,midg; midg,igrid,midg 1.6375020E-09 7.2396702E-09 1,midg,midg; igrid,midg,midg 1.2914869E-09 9.6825152E-09 gauss-seidel spectral radius is 0.9869330 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 13:21:01 rms-change max change #iterations 0.1333458 20.26633 at 10iterations 1.2648705E-02 1.719833 at 20iterations 1.2166712E-03 0.1717453 at 30iterations 1.1469315E-04 1.9069672E-02 at 40iterations 1.1144721E-05 1.7514229E-03 at 50iterations finished qdiffx linear iterations at : 13:21:12 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.1144721E-05 1.7514229E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 13:21:13 4.194u 0.330s 0:14.85 30.4% 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 Sat Oct 15 2011 at 13:21:15 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 1.889062 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): -12.36600 37.15300 ymin,ymax (A): -22.25000 34.28600 zmin,zma (A): -12.19900 40.80300 x,y,z range (A): 49.51900 56.53600 53.00200 scale (grids/A): 1.889062 object centre (A): 12.39350 6.018000 14.30200 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.5399 centred at (gu) : 92.27110 88.18188 90.52461 assigned negative charge : -386.0156 centred at (gu) : 92.15540 88.06546 90.52597 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 71980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22102 grid for indexing accessible points = 1.400000 m= 23679 mr = 48966 m= 3691 mr = 16936 m= 229 mr = 2271 m= 0 mr = 107 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1040 time to turn everything in is 0.6500000 number of dielectric boundary points 31299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19054 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) : 0.6296873 object centre at (A) : 12.39350 6.018000 14.30200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3768503E-03 -1.1752221E-02 midg,1,midg; midg,igrid,midg 4.0165626E-02 -8.3928299E-04 1,midg,midg; igrid,midg,midg -1.0309861E-02 5.2317064E-03 gauss-seidel spectral radius is 0.9986045 estimated iterations to convergence 212 setup time was (sec) 0.9500000 now iterating at: 13:21:19 rms-change max change #iterations 4.115367 177.1967 at 10iterations 1.907914 60.80337 at 20iterations 0.8861974 28.17744 at 30iterations 0.4112475 14.19244 at 40iterations 0.1901429 6.088326 at 50iterations 8.8406205E-02 2.926497 at 60iterations 4.0917404E-02 1.332386 at 70iterations 1.9057909E-02 0.6629124 at 80iterations 8.8236677E-03 0.2857056 at 90iterations 4.0953057E-03 0.1373901 at 100iterations 1.9023340E-03 6.1477661E-02 at 110iterations 8.7915600E-04 2.8041840E-02 at 120iterations finished qdiffx linear iterations at : 13:21:38 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 8.7915600E-04 2.8041840E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 13:21:40 9.835u 0.331s 0:24.83 40.9% 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 Sat Oct 15 2011 at 13:21:41 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2576 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 2.833593 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): -12.36600 37.15300 ymin,ymax (A): -22.25000 34.28600 zmin,zma (A): -12.19900 40.80300 x,y,z range (A): 49.51900 56.53600 53.00200 scale (grids/A): 2.833593 object centre (A): 12.39350 6.018000 14.30200 number of atom coordinates read : 2576 total number of charged atoms : 2430 net assigned charge : 4.525008 assigned positive charge : 390.5399 centred at (gu) : 93.40672 87.27267 90.78703 assigned negative charge : -386.0156 centred at (gu) : 93.23314 87.09827 90.78896 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 166912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22102 grid for indexing accessible points = 1.400000 m= 78702 mr = 119511 m= 26371 mr = 63314 m= 6513 mr = 20657 m= 1056 mr = 4918 m= 57 mr = 766 m= 0 mr = 35 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 3360 time to turn everything in is 1.650000 number of dielectric boundary points 70410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 19439 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) : 1.889062 object centre at (A) : 12.39350 6.018000 14.30200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1839045 -0.3117888 midg,1,midg; midg,igrid,midg 0.4037530 0.1090114 1,midg,midg; igrid,midg,midg -0.2257473 6.4296886E-02 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 1.980000 now iterating at: 13:21:45 rms-change max change #iterations 9.778549 313.4729 at 10iterations 5.665159 120.6399 at 20iterations 3.264618 69.29408 at 30iterations 1.874917 40.18256 at 40iterations 1.073196 21.46301 at 50iterations 0.6157274 11.25983 at 60iterations 0.3519820 6.388317 at 70iterations 0.2021039 3.830488 at 80iterations 0.1154974 2.102955 at 90iterations 6.5921828E-02 1.304873 at 100iterations 3.7745409E-02 0.6950302 at 110iterations 2.1596951E-02 0.4144959 at 120iterations 1.2341533E-02 0.2268181 at 130iterations 7.0506455E-03 0.1283588 at 140iterations 4.0268125E-03 7.7987909E-02 at 150iterations 2.3025337E-03 4.1763306E-02 at 160iterations 1.3157810E-03 2.5400162E-02 at 170iterations 7.5211737E-04 1.4133453E-02 at 180iterations finished qdiffx linear iterations at : 13:22:17 total time elapsed so far: 16.45000 # loops : 180 mean,max change (kT/e) : 7.5211737E-04 1.4133453E-02 energy calculations done at 16.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.64000 DelPhi exited at 13:22:17 16.637u 0.377s 0:36.37 46.7% 0+0k 0+0io 0pf+0w