Mon Oct 10 19:37:42 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 19:37:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: HIR 100 has a net charge of 0.5140 !!! WARNING: HIR 226 has a net charge of 0.5140 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: 0.6034512 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): -24.12500 24.80100 ymin,ymax (A): -21.63000 34.00600 zmin,zma (A): 6.141000 65.13500 x,y,z range (A): 48.92600 55.63600 58.99400 scale (grids/A): 0.6034512 object centre (A): 0.3379993 6.188001 35.63800 number of atom coordinates read : 2667 total number of charged atoms : 2529 net assigned charge : 7.528040 assigned positive charge : 396.4475 centred at (gu) : 90.90331 87.77523 92.50676 assigned negative charge : -388.9208 centred at (gu) : 90.80293 87.79667 92.52518 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6526 nv = 96 ne = 84 npr = 53190 no. pairs analyzed = 53190 no. exposed pairs = 3594 no. arc points = 24950 no. surface atoms = 1211 nbur = 1456 mkacc time = 9.0000004E-02 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 = 1.456000 m= 301 mr = 3350 m= 0 mr = 23 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2000000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2486 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4693765E-09 4.7943440E-09 midg,1,midg; midg,igrid,midg 7.1885689E-09 1.6581378E-09 1,midg,midg; igrid,midg,midg -4.1965995E-10 9.1866657E-09 gauss-seidel spectral radius is 0.9857981 estimated iterations to convergence 69 setup time was (sec) 0.3800000 now iterating at: 19:37:42 rms-change max change #iterations 0.1122551 17.50418 at 10iterations 9.8036351E-03 1.457546 at 20iterations 8.5333391E-04 0.1561999 at 30iterations 8.0322745E-05 1.2687683E-02 at 40iterations 8.4366075E-06 1.3089180E-03 at 50iterations finished qdiffx linear iterations at : 19:37:45 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 8.4366075E-06 1.3089180E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 19:37:46 3.367u 0.171s 0:03.87 91.2% 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 19:37:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: HIR 100 has a net charge of 0.5140 !!! WARNING: HIR 226 has a net charge of 0.5140 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: 1.810354 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): -24.12500 24.80100 ymin,ymax (A): -21.63000 34.00600 zmin,zma (A): 6.141000 65.13500 x,y,z range (A): 48.92600 55.63600 58.99400 scale (grids/A): 1.810354 object centre (A): 0.3379993 6.188001 35.63800 number of atom coordinates read : 2667 total number of charged atoms : 2529 net assigned charge : 7.528040 assigned positive charge : 396.4475 centred at (gu) : 92.70934 83.32506 97.51943 assigned negative charge : -388.9208 centred at (gu) : 92.40860 83.38995 97.57560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24950 grid for indexing accessible points = 1.400000 m= 23516 mr = 47731 m= 3108 mr = 16436 m= 137 mr = 1707 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.3500000 number of dielectric boundary points 32125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19773 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) : 0.6034512 object centre at (A) : 0.3379993 6.188001 35.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1492915E-02 3.3844933E-02 midg,1,midg; midg,igrid,midg -3.1540373E-03 4.1859774E-03 1,midg,midg; igrid,midg,midg 1.6136082E-02 2.1675315E-02 gauss-seidel spectral radius is 0.9985002 estimated iterations to convergence 205 setup time was (sec) 0.5500000 now iterating at: 19:37:47 rms-change max change #iterations 3.823641 184.6993 at 10iterations 1.712240 68.37263 at 20iterations 0.7742284 28.41497 at 30iterations 0.3482992 11.27845 at 40iterations 0.1572269 5.287029 at 50iterations 7.0914567E-02 2.444124 at 60iterations 3.1874187E-02 1.019333 at 70iterations 1.4452282E-02 0.4561286 at 80iterations 6.5430054E-03 0.2201767 at 90iterations 2.9504551E-03 9.5014572E-02 at 100iterations 1.3333148E-03 4.7212601E-02 at 110iterations 6.0357846E-04 1.8768311E-02 at 120iterations finished qdiffx linear iterations at : 19:37:54 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 6.0357846E-04 1.8768311E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 19:37:54 7.719u 0.205s 0:08.41 94.0% 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 19:37:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2667 !!! WARNING: HIR 100 has a net charge of 0.5140 !!! WARNING: HIR 226 has a net charge of 0.5140 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: 2.715530 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): -24.12500 24.80100 ymin,ymax (A): -21.63000 34.00600 zmin,zma (A): 6.141000 65.13500 x,y,z range (A): 48.92600 55.63600 58.99400 scale (grids/A): 2.715530 object centre (A): 0.3379993 6.188001 35.63800 number of atom coordinates read : 2667 total number of charged atoms : 2529 net assigned charge : 7.528040 assigned positive charge : 396.4475 centred at (gu) : 94.06380 79.98743 101.2792 assigned negative charge : -388.9208 centred at (gu) : 93.61292 80.08489 101.3633 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 165393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24950 grid for indexing accessible points = 1.400000 m= 77897 mr = 117113 m= 25545 mr = 61457 m= 5159 mr = 19675 m= 575 mr = 3580 m= 23 mr = 332 m= 0 mr = 9 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 1235 time to turn everything in is 0.8800000 number of dielectric boundary points 72426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 20228 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) : 1.810354 object centre at (A) : 0.3379993 6.188001 35.63800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3687733 0.7906355 midg,1,midg; midg,igrid,midg -7.5724699E-02 0.1163399 1,midg,midg; igrid,midg,midg 0.2980845 0.1518847 gauss-seidel spectral radius is 0.9992323 estimated iterations to convergence 285 setup time was (sec) 1.120000 now iterating at: 19:37:56 rms-change max change #iterations 9.511347 291.7696 at 10iterations 5.572556 149.1263 at 20iterations 3.238920 70.81789 at 30iterations 1.867723 37.13314 at 40iterations 1.076825 22.52783 at 50iterations 0.6181079 13.26931 at 60iterations 0.3537769 8.157304 at 70iterations 0.2024091 4.053083 at 80iterations 0.1157188 2.479256 at 90iterations 6.5856777E-02 1.303616 at 100iterations 3.7608135E-02 0.7031279 at 110iterations 2.1393834E-02 0.4393730 at 120iterations 1.2204782E-02 0.2226033 at 130iterations 6.9534052E-03 0.1335974 at 140iterations 3.9641308E-03 7.9059601E-02 at 150iterations 2.2609467E-03 4.3289185E-02 at 160iterations 1.2877060E-03 2.4669647E-02 at 170iterations 7.3773396E-04 1.4292717E-02 at 180iterations finished qdiffx linear iterations at : 19:38:07 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 7.3773396E-04 1.4292717E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 19:38:07 12.534u 0.210s 0:13.04 97.6% 0+0k 0+0io 0pf+0w