Sat Oct 8 18:11:01 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 Sat Oct 8 2011 at 18:11:02 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 = 4704 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: 0.4966518 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): -0.9550000 62.11000 ymin,ymax (A): -30.01000 31.50400 zmin,zma (A): -22.24100 49.43900 x,y,z range (A): 63.06500 61.51400 71.68000 scale (grids/A): 0.4966518 object centre (A): 30.57750 0.7469997 13.59900 number of atom coordinates read : 4704 total number of charged atoms : 4549 net assigned charge : -11.99997 assigned positive charge : 717.5419 centred at (gu) : 90.58928 91.05662 89.86684 assigned negative charge : -729.5471 centred at (gu) : 90.59644 91.01404 89.86517 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7510 nv = 96 ne = 84 npr = 91821 no. pairs analyzed = 91821 no. exposed pairs = 6308 no. arc points = 43869 no. surface atoms = 2094 nbur = 2610 mkacc time = 0.1600000 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 = 1.708000 m= 264 mr = 3677 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 674 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10054 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6128890E-11 -8.5000729E-11 midg,1,midg; midg,igrid,midg -1.1464449E-10 -3.8292248E-11 1,midg,midg; igrid,midg,midg -6.8746189E-11 -1.1772647E-10 gauss-seidel spectral radius is 0.9792805 estimated iterations to convergence 58 setup time was (sec) 0.5200000 now iterating at: 18:11:02 rms-change max change #iterations 5.7078958E-02 9.202244 at 10iterations 3.1206706E-03 0.5088005 at 20iterations 3.3134859E-04 6.4630508E-02 at 30iterations 7.8072298E-05 1.4380455E-02 at 40iterations 2.0548279E-05 3.6630630E-03 at 50iterations finished qdiffx linear iterations at : 18:11:06 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 2.0548279E-05 3.6630630E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 18:11:06 4.036u 0.266s 0:04.57 93.8% 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 Sat Oct 8 2011 at 18:11:06 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 = 4704 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: 1.489955 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): -0.9550000 62.11000 ymin,ymax (A): -30.01000 31.50400 zmin,zma (A): -22.24100 49.43900 x,y,z range (A): 63.06500 61.51400 71.68000 scale (grids/A): 1.489955 object centre (A): 30.57750 0.7469997 13.59900 number of atom coordinates read : 4704 total number of charged atoms : 4549 net assigned charge : -11.99997 assigned positive charge : 717.5419 centred at (gu) : 91.76618 93.16831 89.59881 assigned negative charge : -729.5471 centred at (gu) : 91.78911 93.04200 89.59537 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 84635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 23591 mr = 56114 m= 1798 mr = 15025 m= 28 mr = 677 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 134 time to turn everything in is 0.4300000 number of dielectric boundary points 38236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 642 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 33867 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) : 0.4966518 object centre at (A) : 30.57750 0.7469997 13.59900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.6502562E-04 -1.7417176E-02 midg,1,midg; midg,igrid,midg -1.2333317E-02 -7.5152596E-03 1,midg,midg; igrid,midg,midg 3.8317856E-03 -2.2050028E-03 gauss-seidel spectral radius is 0.9979928 estimated iterations to convergence 177 setup time was (sec) 0.6800000 now iterating at: 18:11:07 rms-change max change #iterations 3.538758 182.9135 at 10iterations 1.407480 52.05335 at 20iterations 0.5580672 21.80552 at 30iterations 0.2225685 7.394975 at 40iterations 8.8869922E-02 2.766682 at 50iterations 3.5569683E-02 1.123287 at 60iterations 1.4243060E-02 0.4776955 at 70iterations 5.6771315E-03 0.1836233 at 80iterations 2.3022206E-03 7.1294308E-02 at 90iterations 9.4081386E-04 3.1654358E-02 at 100iterations 3.9589655E-04 1.3840675E-02 at 110iterations 1.7487686E-04 6.6280365E-03 at 120iterations finished qdiffx linear iterations at : 18:11:15 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 1.7487686E-04 6.6280365E-03 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 18:11:15 8.389u 0.218s 0:08.88 96.7% 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 8 2011 at 18:11:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4704 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: 2.234933 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): -0.9550000 62.11000 ymin,ymax (A): -30.01000 31.50400 zmin,zma (A): -22.24100 49.43900 x,y,z range (A): 63.06500 61.51400 71.68000 scale (grids/A): 2.234933 object centre (A): 30.57750 0.7469997 13.59900 number of atom coordinates read : 4704 total number of charged atoms : 4549 net assigned charge : -11.99997 assigned positive charge : 717.5419 centred at (gu) : 92.64899 94.75208 89.39787 assigned negative charge : -729.5471 centred at (gu) : 92.68339 94.56286 89.39305 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 197253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43869 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 85682 mr = 138837 m= 20217 mr = 65123 m= 2395 mr = 13986 m= 88 mr = 1298 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 483 time to turn everything in is 1.060000 number of dielectric boundary points 86387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 36250 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) : 1.489955 object centre at (A) : 30.57750 0.7469997 13.59900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1505658 -0.2463263 midg,1,midg; midg,igrid,midg -0.2955039 -0.1326397 1,midg,midg; igrid,midg,midg 8.3797961E-02 -7.7829078E-02 gauss-seidel spectral radius is 0.9991246 estimated iterations to convergence 267 setup time was (sec) 1.350000 now iterating at: 18:11:17 rms-change max change #iterations 9.960588 298.1078 at 10iterations 5.693265 153.7273 at 20iterations 3.216997 76.26756 at 30iterations 1.805265 44.59936 at 40iterations 1.006188 20.38669 at 50iterations 0.5602603 12.16011 at 60iterations 0.3099676 6.512506 at 70iterations 0.1708929 3.417123 at 80iterations 9.4444603E-02 2.054773 at 90iterations 5.2086093E-02 0.9980192 at 100iterations 2.8656581E-02 0.5780373 at 110iterations 1.5727894E-02 0.3118229 at 120iterations 8.6605968E-03 0.1839790 at 130iterations 4.7517158E-03 9.6024036E-02 at 140iterations 2.6061896E-03 4.9522400E-02 at 150iterations 1.4312267E-03 2.7045250E-02 at 160iterations 7.8378862E-04 1.4372826E-02 at 170iterations 4.3020639E-04 7.9317093E-03 at 180iterations finished qdiffx linear iterations at : 18:11:30 total time elapsed so far: 14.23000 # loops : 180 mean,max change (kT/e) : 4.3020639E-04 7.9317093E-03 energy calculations done at 14.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.36000 DelPhi exited at 18:11:30 14.365u 0.282s 0:14.91 98.1% 0+0k 0+0io 0pf+0w