Tue Oct 11 06:37:22 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 06:37:22 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7102669 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): -20.68500 24.64500 ymin,ymax (A): -28.56900 11.08300 zmin,zma (A): -13.47200 36.65000 x,y,z range (A): 45.33000 39.65200 50.12200 scale (grids/A): 0.7102669 object centre (A): 1.980000 -8.743000 11.58900 number of atom coordinates read : 2071 total number of charged atoms : 1943 net assigned charge : 5.931010 assigned positive charge : 314.7340 centred at (gu) : 90.16463 90.64252 89.22643 assigned negative charge : -308.8031 centred at (gu) : 90.01526 90.62224 89.15924 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7080 nv = 96 ne = 84 npr = 41804 no. pairs analyzed = 41804 no. exposed pairs = 2495 no. arc points = 16855 no. surface atoms = 854 nbur = 1217 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4087 m= 9 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1699 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7922 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0880607E-08 7.6231139E-08 midg,1,midg; midg,igrid,midg 3.8234013E-08 7.2478080E-08 1,midg,midg; igrid,midg,midg -2.4436966E-08 1.3449458E-07 gauss-seidel spectral radius is 0.9896634 estimated iterations to convergence 80 setup time was (sec) 0.4700000 now iterating at: 06:37:23 rms-change max change #iterations 0.2042306 28.45780 at 10iterations 2.6211539E-02 3.580724 at 20iterations 3.5572336E-03 0.4724350 at 30iterations 5.9510022E-04 8.3633423E-02 at 40iterations 1.5040862E-04 2.1652222E-02 at 50iterations finished qdiffx linear iterations at : 06:37:25 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 1.5040862E-04 2.1652222E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:37:26 3.062u 0.148s 0:03.56 89.8% 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 06:37:26 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.130801 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): -20.68500 24.64500 ymin,ymax (A): -28.56900 11.08300 zmin,zma (A): -13.47200 36.65000 x,y,z range (A): 45.33000 39.65200 50.12200 scale (grids/A): 2.130801 object centre (A): 1.980000 -8.743000 11.58900 number of atom coordinates read : 2071 total number of charged atoms : 1943 net assigned charge : 5.931010 assigned positive charge : 314.7340 centred at (gu) : 90.49403 91.92770 87.67934 assigned negative charge : -308.8031 centred at (gu) : 90.04557 91.86683 87.47791 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 75122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16855 grid for indexing accessible points = 1.400000 m= 29937 mr = 53667 m= 5752 mr = 22762 m= 538 mr = 3782 m= 11 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 15423 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) : 0.7102669 object centre at (A) : 1.980000 -8.743000 11.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3025663E-02 4.0528178E-02 midg,1,midg; midg,igrid,midg 4.9873758E-03 3.2993410E-02 1,midg,midg; igrid,midg,midg 1.2775075E-02 3.5200685E-02 gauss-seidel spectral radius is 0.9988366 estimated iterations to convergence 232 setup time was (sec) 0.7800000 now iterating at: 06:37:27 rms-change max change #iterations 4.589899 178.5659 at 10iterations 2.275922 72.05193 at 20iterations 1.133805 33.19983 at 30iterations 0.5631418 17.83801 at 40iterations 0.2803487 8.931123 at 50iterations 0.1399406 4.257572 at 60iterations 6.9618933E-02 2.196991 at 70iterations 3.4689128E-02 1.102581 at 80iterations 1.7373068E-02 0.5230637 at 90iterations 8.7472731E-03 0.2697935 at 100iterations 4.4100457E-03 0.1335754 at 110iterations 2.2674855E-03 6.9929123E-02 at 120iterations finished qdiffx linear iterations at : 06:37:33 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 2.2674855E-03 6.9929123E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 06:37:34 7.319u 0.180s 0:07.90 94.8% 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 06:37:34 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2071 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.196201 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): -20.68500 24.64500 ymin,ymax (A): -28.56900 11.08300 zmin,zma (A): -13.47200 36.65000 x,y,z range (A): 45.33000 39.65200 50.12200 scale (grids/A): 3.196201 object centre (A): 1.980000 -8.743000 11.58900 number of atom coordinates read : 2071 total number of charged atoms : 1943 net assigned charge : 5.931010 assigned positive charge : 314.7340 centred at (gu) : 90.74100 92.89146 86.51904 assigned negative charge : -308.8031 centred at (gu) : 90.06844 92.80016 86.21687 start vw surface at 0.1300000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 173168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16855 grid for indexing accessible points = 1.400000 m= 93709 mr = 129070 m= 37765 mr = 77985 m= 10832 mr = 31171 m= 2186 mr = 8346 m= 271 mr = 1592 m= 12 mr = 188 m= 0 mr = 4 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 69587 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 15544 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) : 2.130801 object centre at (A) : 1.980000 -8.743000 11.58900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5811829 0.3350260 midg,1,midg; midg,igrid,midg 8.0422331E-03 0.2584822 1,midg,midg; igrid,midg,midg 0.2530895 0.2744637 gauss-seidel spectral radius is 0.9992939 estimated iterations to convergence 297 setup time was (sec) 2.000000 now iterating at: 06:37:36 rms-change max change #iterations 10.19946 383.9130 at 10iterations 6.020536 119.5833 at 20iterations 3.559469 81.22765 at 30iterations 2.093606 37.06838 at 40iterations 1.230201 23.64711 at 50iterations 0.7217490 13.04195 at 60iterations 0.4243731 8.175093 at 70iterations 0.2481946 4.330238 at 80iterations 0.1454086 2.683383 at 90iterations 8.5293621E-02 1.626378 at 100iterations 5.0108489E-02 0.8415356 at 110iterations 2.9601090E-02 0.5435600 at 120iterations 1.7567372E-02 0.3315508 at 130iterations 1.0635644E-02 0.1882935 at 140iterations 6.5981778E-03 0.1389160 at 150iterations 4.2424966E-03 8.4239006E-02 at 160iterations 2.8904218E-03 5.6644440E-02 at 170iterations 2.0740868E-03 3.9047241E-02 at 180iterations finished qdiffx linear iterations at : 06:37:45 total time elapsed so far: 11.28000 # loops : 180 mean,max change (kT/e) : 2.0740868E-03 3.9047241E-02 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.46000 DelPhi exited at 06:37:46 11.458u 0.234s 0:12.01 97.2% 0+0k 0+0io 0pf+0w