Tue Nov 22 14:20:36 PST 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 Nov 22 2011 at 14:20:36 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6018292 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): -24.11300 35.04000 ymin,ymax (A): -19.08500 20.47300 zmin,zma (A): -2.485000 38.59300 x,y,z range (A): 59.15300 39.55800 41.07800 scale (grids/A): 0.6018292 object centre (A): 5.463501 0.6940002 18.05400 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 3.000004 assigned positive charge : 292.2239 centred at (gu) : 89.69331 90.30444 90.26273 assigned negative charge : -289.2242 centred at (gu) : 89.69779 90.39170 90.39118 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4781 nv = 96 ne = 84 npr = 39880 no. pairs analyzed = 39880 no. exposed pairs = 2484 no. arc points = 17109 no. surface atoms = 839 nbur = 1123 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 210 mr = 2606 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2300000 number of dielectric boundary points 2376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1769 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7390354E-09 -2.5183280E-09 midg,1,midg; midg,igrid,midg 3.6162919E-09 -1.2394947E-09 1,midg,midg; igrid,midg,midg 1.6220278E-09 1.1769712E-09 gauss-seidel spectral radius is 0.9856558 estimated iterations to convergence 68 setup time was (sec) 0.5000000 now iterating at: 14:20:37 rms-change max change #iterations 9.5492326E-02 17.37590 at 10iterations 8.0672139E-03 1.355210 at 20iterations 6.9946720E-04 0.1234736 at 30iterations 6.0633614E-05 9.6435547E-03 at 40iterations 5.0968106E-06 8.4304810E-04 at 50iterations finished qdiffx linear iterations at : 14:20:42 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 5.0968106E-06 8.4304810E-04 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 14:20:43 3.670u 0.220s 0:07.70 50.5% 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 Tue Nov 22 2011 at 14:20:45 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.805488 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): -24.11300 35.04000 ymin,ymax (A): -19.08500 20.47300 zmin,zma (A): -2.485000 38.59300 x,y,z range (A): 59.15300 39.55800 41.07800 scale (grids/A): 1.805488 object centre (A): 5.463501 0.6940002 18.05400 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 3.000004 assigned positive charge : 292.2239 centred at (gu) : 89.07970 90.91299 90.78796 assigned negative charge : -289.2242 centred at (gu) : 89.09353 91.17513 91.17352 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 51834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17109 grid for indexing accessible points = 1.400000 m= 18720 mr = 35483 m= 2402 mr = 14092 m= 85 mr = 1414 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 897 time to turn everything in is 0.4000000 number of dielectric boundary points 22043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14266 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) : 0.6018292 object centre at (A) : 5.463501 0.6940002 18.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0584056E-03 -5.9220809E-03 midg,1,midg; midg,igrid,midg 2.8882874E-03 -4.3639638E-03 1,midg,midg; igrid,midg,midg 3.9620128E-02 3.2442875E-02 gauss-seidel spectral radius is 0.9984054 estimated iterations to convergence 199 setup time was (sec) 0.7100000 now iterating at: 14:20:47 rms-change max change #iterations 3.276618 142.4148 at 10iterations 1.437048 64.54095 at 20iterations 0.6357698 25.05832 at 30iterations 0.2781232 10.85746 at 40iterations 0.1232764 4.449848 at 50iterations 5.3949002E-02 1.892944 at 60iterations 2.3764372E-02 0.9166825 at 70iterations 1.0440661E-02 0.4161658 at 80iterations 4.6012904E-03 0.1740370 at 90iterations 2.0199041E-03 8.2962483E-02 at 100iterations 8.9656934E-04 3.6318779E-02 at 110iterations 3.9417431E-04 1.4816284E-02 at 120iterations finished qdiffx linear iterations at : 14:21:06 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 3.9417431E-04 1.4816284E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 14:21:07 8.091u 0.264s 0:22.55 37.0% 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 Nov 22 2011 at 14:21:09 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.708231 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): -24.11300 35.04000 ymin,ymax (A): -19.08500 20.47300 zmin,zma (A): -2.485000 38.59300 x,y,z range (A): 59.15300 39.55800 41.07800 scale (grids/A): 2.708231 object centre (A): 5.463501 0.6940002 18.05400 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 3.000004 assigned positive charge : 292.2239 centred at (gu) : 88.61961 91.36942 91.18192 assigned negative charge : -289.2242 centred at (gu) : 88.64032 91.76281 91.76029 start vw surface at 0.1200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 119784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17109 grid for indexing accessible points = 1.400000 m= 61061 mr = 85867 m= 20944 mr = 50522 m= 4023 mr = 16993 m= 325 mr = 2937 m= 7 mr = 159 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2991 time to turn everything in is 0.9700000 number of dielectric boundary points 49666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 14639 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) : 1.805488 object centre at (A) : 5.463501 0.6940002 18.05400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7366136E-02 -5.9411291E-02 midg,1,midg; midg,igrid,midg 1.8380392E-02 -3.9068174E-02 1,midg,midg; igrid,midg,midg 0.4564646 0.2716098 gauss-seidel spectral radius is 0.9991761 estimated iterations to convergence 275 setup time was (sec) 1.270000 now iterating at: 14:21:16 rms-change max change #iterations 7.901207 252.2147 at 10iterations 4.478523 127.2739 at 20iterations 2.516083 63.96461 at 30iterations 1.409359 38.84589 at 40iterations 0.7875800 18.97854 at 50iterations 0.4394275 9.404931 at 60iterations 0.2442542 5.428615 at 70iterations 0.1363729 3.483803 at 80iterations 7.5922668E-02 1.735075 at 90iterations 4.2221952E-02 0.8597374 at 100iterations 2.3504337E-02 0.5304031 at 110iterations 1.3110292E-02 0.2714176 at 120iterations 7.2686989E-03 0.1677666 at 130iterations 4.0530525E-03 9.0515137E-02 at 140iterations 2.2535014E-03 4.8785925E-02 at 150iterations 1.2515989E-03 3.1084061E-02 at 160iterations 6.9711520E-04 1.4608383E-02 at 170iterations 3.8749847E-04 7.9221725E-03 at 180iterations finished qdiffx linear iterations at : 14:21:45 total time elapsed so far: 11.12000 # loops : 180 mean,max change (kT/e) : 3.8749847E-04 7.9221725E-03 energy calculations done at 11.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 14:21:47 11.307u 0.152s 0:38.08 30.0% 0+0k 0+0io 0pf+0w