Sat Oct 15 12:21:28 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 15 2011 at 12:21:28 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4480 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.4404741 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): -2.799000 78.02300 ymin,ymax (A): 0.8119999 66.39700 zmin,zma (A): 175.2530 236.7070 x,y,z range (A): 80.82201 65.58501 61.45401 scale (grids/A): 0.4404741 object centre (A): 37.61200 33.60450 205.9800 number of atom coordinates read : 4480 total number of charged atoms : 4253 net assigned charge : 22.99997 assigned positive charge : 654.3812 centred at (gu) : 85.84948 91.20512 88.77422 assigned negative charge : -631.3859 centred at (gu) : 85.79309 91.17248 88.80372 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5169 nv = 96 ne = 84 npr = 90754 no. pairs analyzed = 90754 no. exposed pairs = 5816 no. arc points = 39911 no. surface atoms = 1979 nbur = 2501 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 = 1.904000 m= 129 mr = 2429 m= 0 mr = 1 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 661 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5351434E-11 4.6206129E-12 midg,1,midg; midg,igrid,midg 4.4974840E-12 1.5565665E-11 1,midg,midg; igrid,midg,midg 1.5821370E-11 3.7209983E-12 gauss-seidel spectral radius is 0.9736922 estimated iterations to convergence 51 setup time was (sec) 0.4800000 now iterating at: 12:21:29 rms-change max change #iterations 3.0399140E-02 6.239239 at 10iterations 3.2345671E-03 0.5662003 at 20iterations 9.3903049E-04 0.1585789 at 30iterations 2.8994621E-04 5.1181793E-02 at 40iterations 9.0479269E-05 1.6429901E-02 at 50iterations finished qdiffx linear iterations at : 12:21:32 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 9.0479269E-05 1.6429901E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 12:21:32 3.634u 0.213s 0:04.30 89.3% 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 12:21:32 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4480 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.321422 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): -2.799000 78.02300 ymin,ymax (A): 0.8119999 66.39700 zmin,zma (A): 175.2530 236.7070 x,y,z range (A): 80.82201 65.58501 61.45401 scale (grids/A): 1.321422 object centre (A): 37.61200 33.60450 205.9800 number of atom coordinates read : 4480 total number of charged atoms : 4253 net assigned charge : 22.99997 assigned positive charge : 654.3812 centred at (gu) : 77.54670 93.61382 86.32040 assigned negative charge : -631.3859 centred at (gu) : 77.37883 93.51711 86.41100 start vw surface at 0.1200000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 59726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 14283 mr = 38879 m= 731 mr = 8642 m= 8 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.3300000 number of dielectric boundary points 27069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 714 ## 27 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 30009 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) : 0.4404741 object centre at (A) : 37.61200 33.60450 205.9800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4762769E-03 8.0750120E-04 midg,1,midg; midg,igrid,midg 3.1999673E-03 5.8085746E-03 1,midg,midg; igrid,midg,midg 2.5844628E-02 2.7742244E-03 gauss-seidel spectral radius is 0.9973072 estimated iterations to convergence 154 setup time was (sec) 0.5700000 now iterating at: 12:21:33 rms-change max change #iterations 2.458214 128.5016 at 10iterations 0.8451441 32.32069 at 20iterations 0.2941714 12.51147 at 30iterations 0.1013891 4.278122 at 40iterations 3.5398975E-02 1.419891 at 50iterations 1.2521666E-02 0.5277824 at 60iterations 4.6962164E-03 0.1958523 at 70iterations 2.0067410E-03 7.8933716E-02 at 80iterations 1.0488097E-03 4.4124603E-02 at 90iterations 6.5586541E-04 2.6166916E-02 at 100iterations 4.4057230E-04 1.6906738E-02 at 110iterations 3.0461332E-04 1.2027740E-02 at 120iterations finished qdiffx linear iterations at : 12:21:40 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 3.0461332E-04 1.2027740E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 12:21:41 7.824u 0.202s 0:08.37 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 Sat Oct 15 2011 at 12:21:41 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4480 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.982133 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): -2.799000 78.02300 ymin,ymax (A): 0.8119999 66.39700 zmin,zma (A): 175.2530 236.7070 x,y,z range (A): 80.82201 65.58501 61.45401 scale (grids/A): 1.982133 object centre (A): 37.61200 33.60450 205.9800 number of atom coordinates read : 4480 total number of charged atoms : 4253 net assigned charge : 22.99997 assigned positive charge : 654.3812 centred at (gu) : 71.31970 95.42042 84.48035 assigned negative charge : -631.3859 centred at (gu) : 71.06812 95.27553 84.61643 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 140067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 54507 mr = 97270 m= 10558 mr = 40415 m= 831 mr = 6865 m= 13 mr = 347 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.7400000 number of dielectric boundary points 61080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 33602 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) : 1.321422 object centre at (A) : 37.61200 33.60450 205.9800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1146775 1.4791490E-02 midg,1,midg; midg,igrid,midg 8.5019335E-02 0.1387640 1,midg,midg; igrid,midg,midg 0.6325060 3.9718561E-02 gauss-seidel spectral radius is 0.9988673 estimated iterations to convergence 235 setup time was (sec) 0.9600000 now iterating at: 12:21:42 rms-change max change #iterations 7.290278 238.8982 at 10iterations 3.767530 97.22694 at 20iterations 1.943808 54.51317 at 30iterations 0.9929801 23.46582 at 40iterations 0.5064057 12.38082 at 50iterations 0.2583455 6.645391 at 60iterations 0.1309540 3.126286 at 70iterations 6.6413276E-02 1.693028 at 80iterations 3.3609256E-02 0.8338814 at 90iterations 1.7072417E-02 0.3951755 at 100iterations 8.7005133E-03 0.2006431 at 110iterations 4.4782311E-03 9.9464417E-02 at 120iterations 2.3527720E-03 5.4548264E-02 at 130iterations 1.2977385E-03 3.1873703E-02 at 140iterations 7.6801557E-04 1.8815994E-02 at 150iterations 4.9942883E-04 1.3057709E-02 at 160iterations 3.5231892E-04 8.6059570E-03 at 170iterations 2.6277924E-04 6.3266754E-03 at 180iterations finished qdiffx linear iterations at : 12:21:53 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 2.6277924E-04 6.3266754E-03 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 12:21:54 12.429u 0.245s 0:12.99 97.4% 0+0k 0+0io 0pf+0w