Tue Oct 11 03:13:20 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 Tue Oct 11 2011 at 03:13:20 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 = 2016 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: 0.6263416 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): -26.55100 23.71800 ymin,ymax (A): -21.68100 22.70700 zmin,zma (A): -24.79500 32.04300 x,y,z range (A): 50.26900 44.38800 56.83800 scale (grids/A): 0.6263416 object centre (A): -1.416499 0.5129995 3.624000 number of atom coordinates read : 2016 total number of charged atoms : 1875 net assigned charge : 4.000013 assigned positive charge : 291.6078 centred at (gu) : 92.12394 90.10535 88.38016 assigned negative charge : -287.6083 centred at (gu) : 92.19520 90.03805 88.48902 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5544 nv = 96 ne = 84 npr = 39515 no. pairs analyzed = 39515 no. exposed pairs = 2810 no. arc points = 20749 no. surface atoms = 938 nbur = 1078 mkacc time = 5.9999995E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 2762 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1954 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4515082E-08 -1.7704812E-09 midg,1,midg; midg,igrid,midg -1.1236743E-10 7.9523232E-09 1,midg,midg; igrid,midg,midg 5.0791185E-09 -7.3370215E-10 gauss-seidel spectral radius is 0.9867576 estimated iterations to convergence 71 setup time was (sec) 0.3700000 now iterating at: 03:13:21 rms-change max change #iterations 0.1116370 19.20558 at 10iterations 1.0184702E-02 1.645424 at 20iterations 9.5197331E-04 0.1901913 at 30iterations 8.8531640E-05 1.6004086E-02 at 40iterations 8.4480171E-06 1.3980865E-03 at 50iterations finished qdiffx linear iterations at : 03:13:24 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.4480171E-06 1.3980865E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:13:24 3.423u 0.165s 0:03.95 90.6% 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 Tue Oct 11 2011 at 03:13:24 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 = 2016 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: 1.879025 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): -26.55100 23.71800 ymin,ymax (A): -21.68100 22.70700 zmin,zma (A): -24.79500 32.04300 x,y,z range (A): 50.26900 44.38800 56.83800 scale (grids/A): 1.879025 object centre (A): -1.416499 0.5129995 3.624000 number of atom coordinates read : 2016 total number of charged atoms : 1875 net assigned charge : 4.000013 assigned positive charge : 291.6078 centred at (gu) : 96.37173 90.31622 85.14039 assigned negative charge : -287.6083 centred at (gu) : 96.58582 90.11430 85.46716 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58672 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20749 grid for indexing accessible points = 1.400000 m= 20159 mr = 37939 m= 2988 mr = 13997 m= 134 mr = 1620 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 28371 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14740 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) : 0.6263416 object centre at (A) : -1.416499 0.5129995 3.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5156662E-02 -2.9544676E-02 midg,1,midg; midg,igrid,midg -6.6201449E-03 7.4930442E-03 1,midg,midg; igrid,midg,midg 1.4840603E-02 5.1946510E-03 gauss-seidel spectral radius is 0.9985471 estimated iterations to convergence 208 setup time was (sec) 0.5200000 now iterating at: 03:13:25 rms-change max change #iterations 3.480239 181.6469 at 10iterations 1.586514 63.39809 at 20iterations 0.7221253 30.14941 at 30iterations 0.3296848 11.90556 at 40iterations 0.1496675 5.534630 at 50iterations 6.8327837E-02 2.393486 at 60iterations 3.1157184E-02 1.299088 at 70iterations 1.4194382E-02 0.6222492 at 80iterations 6.5032924E-03 0.2311223 at 90iterations 2.9566935E-03 0.1040547 at 100iterations 1.3474372E-03 5.0220490E-02 at 110iterations 6.1533746E-04 2.0324707E-02 at 120iterations finished qdiffx linear iterations at : 03:13:32 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 6.1533746E-04 2.0324707E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 03:13:33 7.809u 0.204s 0:08.35 95.8% 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 Oct 11 2011 at 03:13:33 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 = 2016 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: 2.818537 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): -26.55100 23.71800 ymin,ymax (A): -21.68100 22.70700 zmin,zma (A): -24.79500 32.04300 x,y,z range (A): 50.26900 44.38800 56.83800 scale (grids/A): 2.818537 object centre (A): -1.416499 0.5129995 3.624000 number of atom coordinates read : 2016 total number of charged atoms : 1875 net assigned charge : 4.000013 assigned positive charge : 291.6078 centred at (gu) : 99.55733 90.47440 82.71043 assigned negative charge : -287.6083 centred at (gu) : 99.87884 90.17145 83.20066 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 135381 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20749 grid for indexing accessible points = 1.400000 m= 64734 mr = 92260 m= 23008 mr = 51249 m= 5096 mr = 17605 m= 615 mr = 3485 m= 44 mr = 306 m= 0 mr = 10 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 63963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 14999 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) : 1.879025 object centre at (A) : -1.416499 0.5129995 3.624000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3192461 -0.4542335 midg,1,midg; midg,igrid,midg -6.7585014E-02 6.7346118E-02 1,midg,midg; igrid,midg,midg 0.1433184 7.6673128E-02 gauss-seidel spectral radius is 0.9992389 estimated iterations to convergence 286 setup time was (sec) 1.000000 now iterating at: 03:13:34 rms-change max change #iterations 8.492761 413.9884 at 10iterations 4.966785 135.6069 at 20iterations 2.874495 77.18914 at 30iterations 1.659236 40.95329 at 40iterations 0.9574001 20.54164 at 50iterations 0.5488194 12.47029 at 60iterations 0.3155345 7.400467 at 70iterations 0.1800300 4.039183 at 80iterations 0.1028785 2.378431 at 90iterations 5.8731247E-02 1.377292 at 100iterations 3.3554640E-02 0.7265368 at 110iterations 1.9107567E-02 0.3839080 at 120iterations 1.0894041E-02 0.2272043 at 130iterations 6.2026302E-03 0.1292572 at 140iterations 3.5275670E-03 6.7630768E-02 at 150iterations 2.0113930E-03 3.9354920E-02 at 160iterations 1.1473503E-03 2.3315430E-02 at 170iterations 6.5370073E-04 1.3752937E-02 at 180iterations finished qdiffx linear iterations at : 03:13:45 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 6.5370073E-04 1.3752937E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 03:13:46 12.328u 0.187s 0:12.80 97.6% 0+0k 0+0io 0pf+0w