Mon Oct 10 18:45:36 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 Mon Oct 10 2011 at 18:45:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2302 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: 0.6937814 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): 28.26600 73.12200 ymin,ymax (A): 17.39800 68.71100 zmin,zma (A): 5.656000 56.11800 x,y,z range (A): 44.85600 51.31300 50.46200 scale (grids/A): 0.6937814 object centre (A): 50.69400 43.05450 30.88700 number of atom coordinates read : 2302 total number of charged atoms : 2166 net assigned charge : 2.000004 assigned positive charge : 342.8542 centred at (gu) : 89.22572 86.42979 88.38062 assigned negative charge : -340.8547 centred at (gu) : 89.20747 86.55894 88.34021 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7339 nv = 96 ne = 84 npr = 47989 no. pairs analyzed = 47989 no. exposed pairs = 2927 no. arc points = 20303 no. surface atoms = 980 nbur = 1322 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 4001 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.2900000 number of dielectric boundary points 3766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1870 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8453 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9739815E-09 1.8924011E-08 midg,1,midg; midg,igrid,midg 1.2471668E-07 -1.9734706E-08 1,midg,midg; igrid,midg,midg 3.6080350E-09 1.4975374E-08 gauss-seidel spectral radius is 0.9891981 estimated iterations to convergence 78 setup time was (sec) 0.5200000 now iterating at: 18:45:36 rms-change max change #iterations 0.1945728 25.58600 at 10iterations 2.2547321E-02 3.414696 at 20iterations 2.6584896E-03 0.3379526 at 30iterations 3.2756239E-04 4.0973663E-02 at 40iterations 4.1418032E-05 5.9051514E-03 at 50iterations finished qdiffx linear iterations at : 18:45:39 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 4.1418032E-05 5.9051514E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 18:45:39 3.288u 0.157s 0:03.78 90.7% 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 Mon Oct 10 2011 at 18:45:39 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2302 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: 2.081344 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): 28.26600 73.12200 ymin,ymax (A): 17.39800 68.71100 zmin,zma (A): 5.656000 56.11800 x,y,z range (A): 44.85600 51.31300 50.46200 scale (grids/A): 2.081344 object centre (A): 50.69400 43.05450 30.88700 number of atom coordinates read : 2302 total number of charged atoms : 2166 net assigned charge : 2.000004 assigned positive charge : 342.8542 centred at (gu) : 87.67654 79.28915 85.14141 assigned negative charge : -340.8547 centred at (gu) : 87.62228 79.67677 85.02034 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77213 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20303 grid for indexing accessible points = 1.400000 m= 30198 mr = 52837 m= 6207 mr = 22539 m= 545 mr = 4102 m= 18 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1341 time to turn everything in is 0.5900000 number of dielectric boundary points 34441 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17208 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) : 0.6937814 object centre at (A) : 50.69400 43.05450 30.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1305942E-02 4.0757686E-02 midg,1,midg; midg,igrid,midg 3.0699767E-02 -2.6239550E-02 1,midg,midg; igrid,midg,midg 1.7677063E-02 6.0085631E-03 gauss-seidel spectral radius is 0.9988112 estimated iterations to convergence 230 setup time was (sec) 0.8800000 now iterating at: 18:45:40 rms-change max change #iterations 4.683006 190.0346 at 10iterations 2.299963 79.71469 at 20iterations 1.131402 33.69505 at 30iterations 0.5597259 18.65993 at 40iterations 0.2759224 8.122911 at 50iterations 0.1355677 3.825316 at 60iterations 6.6912934E-02 1.973364 at 70iterations 3.2909762E-02 0.9387882 at 80iterations 1.6196245E-02 0.4529624 at 90iterations 8.0059180E-03 0.2433338 at 100iterations 3.9439267E-03 0.1133633 at 110iterations 1.9441320E-03 5.6330681E-02 at 120iterations finished qdiffx linear iterations at : 18:45:47 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.9441320E-03 5.6330681E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.460000 DelPhi exited at 18:45:48 7.465u 0.183s 0:08.10 94.3% 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 Mon Oct 10 2011 at 18:45:48 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2302 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.122016 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): 28.26600 73.12200 ymin,ymax (A): 17.39800 68.71100 zmin,zma (A): 5.656000 56.11800 x,y,z range (A): 44.85600 51.31300 50.46200 scale (grids/A): 3.122016 object centre (A): 50.69400 43.05450 30.88700 number of atom coordinates read : 2302 total number of charged atoms : 2166 net assigned charge : 2.000004 assigned positive charge : 342.8542 centred at (gu) : 86.51461 73.93358 82.71205 assigned negative charge : -340.8547 centred at (gu) : 86.43342 74.51511 82.53047 start vw surface at 0.1900000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 177762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20303 grid for indexing accessible points = 1.400000 m= 92531 mr = 127670 m= 39194 mr = 75773 m= 11824 mr = 31996 m= 2294 mr = 9132 m= 276 mr = 1606 m= 14 mr = 162 m= 0 mr = 4 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 4630 time to turn everything in is 1.970000 number of dielectric boundary points 77552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 17328 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) : 2.081344 object centre at (A) : 50.69400 43.05450 30.88700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1923511 0.8103925 midg,1,midg; midg,igrid,midg 0.1873703 -0.2302943 1,midg,midg; igrid,midg,midg 0.2178512 -3.6656469E-02 gauss-seidel spectral radius is 0.9993060 estimated iterations to convergence 299 setup time was (sec) 2.270000 now iterating at: 18:45:50 rms-change max change #iterations 10.67972 528.3335 at 10iterations 6.342513 120.5806 at 20iterations 3.759142 84.74803 at 30iterations 2.226405 43.44678 at 40iterations 1.307954 24.98277 at 50iterations 0.7712272 13.36211 at 60iterations 0.4538635 8.568333 at 70iterations 0.2659333 5.742964 at 80iterations 0.1559717 2.581056 at 90iterations 9.1300130E-02 1.684853 at 100iterations 5.3578071E-02 0.9406357 at 110iterations 3.1380828E-02 0.5243669 at 120iterations 1.8351505E-02 0.3207550 at 130iterations 1.0744627E-02 0.1844807 at 140iterations 6.3012806E-03 0.1098022 at 150iterations 3.6815312E-03 6.3848495E-02 at 160iterations 2.1558993E-03 4.0233612E-02 at 170iterations 1.2628506E-03 2.1818161E-02 at 180iterations finished qdiffx linear iterations at : 18:46:01 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.2628506E-03 2.1818161E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 18:46:01 13.121u 0.168s 0:13.57 97.8% 0+0k 0+0io 0pf+0w