Mon Oct 10 09:44:03 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 09:44:03 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 = 2819 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5845169 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): -17.42800 33.83400 ymin,ymax (A): -60.77300 -2.575000 zmin,zma (A): -1.007000 59.89800 x,y,z range (A): 51.26200 58.19800 60.90500 scale (grids/A): 0.5845169 object centre (A): 8.203000 -31.67400 29.44550 number of atom coordinates read : 2819 total number of charged atoms : 2668 net assigned charge : 6.000023 assigned positive charge : 412.4380 centred at (gu) : 88.48101 88.35376 88.26205 assigned negative charge : -406.4383 centred at (gu) : 88.52967 88.24776 88.12765 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6643 nv = 96 ne = 84 npr = 53954 no. pairs analyzed = 53954 no. exposed pairs = 4256 no. arc points = 31138 no. surface atoms = 1404 nbur = 1415 mkacc time = 8.9999996E-02 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 = 1.484000 m= 347 mr = 2932 m= 0 mr = 22 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3032 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8192 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3936753E-09 3.1266336E-09 midg,1,midg; midg,igrid,midg -1.3370136E-09 2.7587463E-09 1,midg,midg; igrid,midg,midg 3.8803796E-09 3.5364286E-10 gauss-seidel spectral radius is 0.9849016 estimated iterations to convergence 67 setup time was (sec) 0.3900000 now iterating at: 09:44:04 rms-change max change #iterations 9.8484986E-02 16.70618 at 10iterations 7.7124769E-03 1.145723 at 20iterations 6.2114070E-04 0.1089802 at 30iterations 5.7856247E-05 8.6007118E-03 at 40iterations 9.2724213E-06 1.1367798E-03 at 50iterations finished qdiffx linear iterations at : 09:44:07 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 9.2724213E-06 1.1367798E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 09:44:07 3.448u 0.184s 0:03.95 91.6% 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 09:44:07 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 = 2819 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.753551 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): -17.42800 33.83400 ymin,ymax (A): -60.77300 -2.575000 zmin,zma (A): -1.007000 59.89800 x,y,z range (A): 51.26200 58.19800 60.90500 scale (grids/A): 1.753551 object centre (A): 8.203000 -31.67400 29.44550 number of atom coordinates read : 2819 total number of charged atoms : 2668 net assigned charge : 6.000023 assigned positive charge : 412.4380 centred at (gu) : 85.44279 85.06055 84.78587 assigned negative charge : -406.4383 centred at (gu) : 85.58864 84.74295 84.38264 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 22071 mr = 42487 m= 3023 mr = 13956 m= 140 mr = 1430 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 37456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 20742 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) : 0.5845169 object centre at (A) : 8.203000 -31.67400 29.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0947603E-02 8.7242071E-03 midg,1,midg; midg,igrid,midg 2.4513727E-02 3.2296542E-02 1,midg,midg; igrid,midg,midg 2.1271188E-02 8.3773900E-03 gauss-seidel spectral radius is 0.9984452 estimated iterations to convergence 201 setup time was (sec) 0.5700000 now iterating at: 09:44:08 rms-change max change #iterations 3.736872 162.9217 at 10iterations 1.664707 67.18919 at 20iterations 0.7371876 35.02656 at 30iterations 0.3291473 11.46610 at 40iterations 0.1462405 4.957764 at 50iterations 6.5002739E-02 2.297354 at 60iterations 2.8885895E-02 1.123489 at 70iterations 1.2879440E-02 0.4789276 at 80iterations 5.7177236E-03 0.2157784 at 90iterations 2.5382882E-03 9.7846985E-02 at 100iterations 1.1349557E-03 3.6842346E-02 at 110iterations 5.0472928E-04 1.8558502E-02 at 120iterations finished qdiffx linear iterations at : 09:44:15 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 5.0472928E-04 1.8558502E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 09:44:16 7.895u 0.204s 0:08.37 96.6% 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 09:44:16 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 = 2819 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.630326 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): -17.42800 33.83400 ymin,ymax (A): -60.77300 -2.575000 zmin,zma (A): -1.007000 59.89800 x,y,z range (A): 51.26200 58.19800 60.90500 scale (grids/A): 2.630326 object centre (A): 8.203000 -31.67400 29.44550 number of atom coordinates read : 2819 total number of charged atoms : 2668 net assigned charge : 6.000023 assigned positive charge : 412.4380 centred at (gu) : 83.16409 82.59071 82.17870 assigned negative charge : -406.4383 centred at (gu) : 83.38286 82.11435 81.57384 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 162068 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31138 grid for indexing accessible points = 1.400000 m= 72013 mr = 105002 m= 23568 mr = 53455 m= 4868 mr = 16773 m= 494 mr = 3034 m= 29 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8700000 number of dielectric boundary points 84555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21331 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) : 1.753551 object centre at (A) : 8.203000 -31.67400 29.44550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2697749 1.8587502E-02 midg,1,midg; midg,igrid,midg 0.5063661 0.4104555 1,midg,midg; igrid,midg,midg 0.2105867 8.6131491E-02 gauss-seidel spectral radius is 0.9992377 estimated iterations to convergence 286 setup time was (sec) 1.090000 now iterating at: 09:44:17 rms-change max change #iterations 9.500253 291.0891 at 10iterations 5.668403 141.5520 at 20iterations 3.323943 92.97512 at 30iterations 1.938614 52.95676 at 40iterations 1.122725 29.88464 at 50iterations 0.6497335 15.96826 at 60iterations 0.3740853 9.616344 at 70iterations 0.2152276 4.681269 at 80iterations 0.1233207 2.834679 at 90iterations 7.0809297E-02 1.719849 at 100iterations 4.0475212E-02 0.9732780 at 110iterations 2.3102691E-02 0.4957024 at 120iterations 1.3205794E-02 0.2673588 at 130iterations 7.5341170E-03 0.1655126 at 140iterations 4.3007904E-03 8.8121891E-02 at 150iterations 2.4510652E-03 5.4468155E-02 at 160iterations 1.3973762E-03 2.8274536E-02 at 170iterations 7.9877791E-04 1.7955780E-02 at 180iterations finished qdiffx linear iterations at : 09:44:28 total time elapsed so far: 12.59000 # loops : 180 mean,max change (kT/e) : 7.9877791E-04 1.7955780E-02 energy calculations done at 12.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 09:44:29 12.721u 0.220s 0:13.22 97.8% 0+0k 0+0io 0pf+0w