Tue Oct 11 03:49:44 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+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 Oct 11 2011 at 03:49:44 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6607153 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): -11.00300 36.65300 ymin,ymax (A): -25.78900 22.67100 zmin,zma (A): -8.522000 45.35900 x,y,z range (A): 47.65600 48.46000 53.88100 scale (grids/A): 0.6607153 object centre (A): 12.82500 -1.559000 18.41850 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 1.154016 assigned positive charge : 413.7698 centred at (gu) : 90.06434 90.20704 91.38233 assigned negative charge : -412.6164 centred at (gu) : 89.81386 90.07814 91.33344 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7958 nv = 96 ne = 84 npr = 56305 no. pairs analyzed = 56305 no. exposed pairs = 3304 no. arc points = 23264 no. surface atoms = 1110 nbur = 1620 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 448 mr = 4551 m= 5 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.3300000 number of dielectric boundary points 3805 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2212 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9422 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7165157E-09 1.7707677E-08 midg,1,midg; midg,igrid,midg -2.4051738E-08 3.1360496E-08 1,midg,midg; igrid,midg,midg -5.1508003E-08 5.5757631E-08 gauss-seidel spectral radius is 0.9881349 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:49:45 rms-change max change #iterations 0.1747490 23.61940 at 10iterations 1.8765144E-02 2.593410 at 20iterations 2.1254055E-03 0.2614453 at 30iterations 2.8581341E-04 5.0682068E-02 at 40iterations 5.6557434E-05 7.6675415E-03 at 50iterations finished qdiffx linear iterations at : 03:49:49 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 5.6557434E-05 7.6675415E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 03:49:50 4.592u 0.402s 0:05.28 94.5% 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 Oct 11 2011 at 03:49:50 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.982146 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): -11.00300 36.65300 ymin,ymax (A): -25.78900 22.67100 zmin,zma (A): -8.522000 45.35900 x,y,z range (A): 47.65600 48.46000 53.88100 scale (grids/A): 1.982146 object centre (A): 12.82500 -1.559000 18.41850 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 1.154016 assigned positive charge : 413.7698 centred at (gu) : 90.19239 90.62054 94.14612 assigned negative charge : -412.6164 centred at (gu) : 89.44141 90.23412 94.00024 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 31958 mr = 60391 m= 5225 mr = 23975 m= 318 mr = 3384 m= 6 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1241 time to turn everything in is 0.7000000 number of dielectric boundary points 34986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 20398 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) : 0.6607153 object centre at (A) : 12.82500 -1.559000 18.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9637830E-02 -2.5324265E-02 midg,1,midg; midg,igrid,midg -1.5029685E-02 2.9087706E-02 1,midg,midg; igrid,midg,midg -1.6213549E-02 7.0884995E-02 gauss-seidel spectral radius is 0.9987464 estimated iterations to convergence 224 setup time was (sec) 1.010000 now iterating at: 03:49:51 rms-change max change #iterations 4.798560 182.8824 at 10iterations 2.322670 70.69680 at 20iterations 1.121510 34.29733 at 30iterations 0.5439900 15.03970 at 40iterations 0.2639368 7.722636 at 50iterations 0.1279493 4.058304 at 60iterations 6.2003352E-02 1.873524 at 70iterations 3.0051395E-02 0.9563255 at 80iterations 1.4534055E-02 0.4493561 at 90iterations 7.0832656E-03 0.2149029 at 100iterations 3.4561108E-03 0.1106396 at 110iterations 1.6969283E-03 5.0877571E-02 at 120iterations finished qdiffx linear iterations at : 03:50:01 total time elapsed so far: 11.13000 # loops : 120 mean,max change (kT/e) : 1.6969283E-03 5.0877571E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 03:50:02 11.287u 0.446s 0:12.25 95.6% 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 03:50:02 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.973219 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): -11.00300 36.65300 ymin,ymax (A): -25.78900 22.67100 zmin,zma (A): -8.522000 45.35900 x,y,z range (A): 47.65600 48.46000 53.88100 scale (grids/A): 2.973219 object centre (A): 12.82500 -1.559000 18.41850 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 1.154016 assigned positive charge : 413.7698 centred at (gu) : 90.28866 90.93060 96.21909 assigned negative charge : -412.6164 centred at (gu) : 89.16218 90.35110 96.00021 start vw surface at 0.1200000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 197193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23264 grid for indexing accessible points = 1.400000 m= 102470 mr = 145959 m= 38381 mr = 84674 m= 9455 mr = 31233 m= 1446 mr = 7266 m= 108 mr = 995 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 4274 time to turn everything in is 1.910000 number of dielectric boundary points 78885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 20617 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) : 1.982146 object centre at (A) : 12.82500 -1.559000 18.41850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7601650 -6.7659825E-02 midg,1,midg; midg,igrid,midg -0.1786493 0.3597125 1,midg,midg; igrid,midg,midg -9.0279758E-02 0.5994421 gauss-seidel spectral radius is 0.9992843 estimated iterations to convergence 295 setup time was (sec) 2.250000 now iterating at: 03:50:05 rms-change max change #iterations 10.96059 415.8812 at 10iterations 6.439665 130.2194 at 20iterations 3.773007 72.85838 at 30iterations 2.209640 42.26928 at 40iterations 1.291491 24.27419 at 50iterations 0.7547963 14.26742 at 60iterations 0.4399601 8.942156 at 70iterations 0.2565189 4.641064 at 80iterations 0.1496055 2.583862 at 90iterations 8.7069899E-02 1.409233 at 100iterations 5.0703984E-02 0.9826622 at 110iterations 2.9548801E-02 0.4963608 at 120iterations 1.7249908E-02 0.3646812 at 130iterations 1.0152610E-02 0.1592784 at 140iterations 5.9899483E-03 0.1075974 at 150iterations 3.5833870E-03 7.2336197E-02 at 160iterations 2.1904795E-03 4.4284821E-02 at 170iterations 1.3764075E-03 2.7046204E-02 at 180iterations finished qdiffx linear iterations at : 03:50:22 total time elapsed so far: 19.21000 # loops : 180 mean,max change (kT/e) : 1.3764075E-03 2.7046204E-02 energy calculations done at 19.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.38000 DelPhi exited at 03:50:23 19.382u 0.476s 0:21.28 93.2% 0+0k 0+0io 0pf+0w