Mon Oct 10 09:08:34 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 09:08:35 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6001248 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): -24.23700 35.08400 ymin,ymax (A): -19.60700 20.21900 zmin,zma (A): -2.689000 38.64500 x,y,z range (A): 59.32100 39.82600 41.33400 scale (grids/A): 0.6001248 object centre (A): 5.423500 0.3059998 17.97800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.73923 90.53145 90.18074 assigned negative charge : -288.4263 centred at (gu) : 89.74101 90.61792 90.31134 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 4772 nv = 96 ne = 84 npr = 40121 no. pairs analyzed = 40121 no. exposed pairs = 2418 no. arc points = 17018 no. surface atoms = 819 nbur = 1145 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 222 mr = 2624 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3000000 number of dielectric boundary points 2344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1801 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 5855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6240070E-09 -2.3959434E-09 midg,1,midg; midg,igrid,midg 3.2333276E-09 -1.2115802E-09 1,midg,midg; igrid,midg,midg 1.4445168E-09 1.1967217E-09 gauss-seidel spectral radius is 0.9855762 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 09:08:35 rms-change max change #iterations 9.7812578E-02 16.44564 at 10iterations 8.1235962E-03 1.527540 at 20iterations 6.7970774E-04 0.1439037 at 30iterations 5.8553454E-05 1.1003494E-02 at 40iterations 4.8751522E-06 7.6293945E-04 at 50iterations finished qdiffx linear iterations at : 09:08:38 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.8751522E-06 7.6293945E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 09:08:38 3.429u 0.167s 0:03.87 92.5% 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 Mon Oct 10 2011 at 09:08:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.800374 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): -24.23700 35.08400 ymin,ymax (A): -19.60700 20.21900 zmin,zma (A): -2.689000 38.64500 x,y,z range (A): 59.32100 39.82600 41.33400 scale (grids/A): 1.800374 object centre (A): 5.423500 0.3059998 17.97800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 89.21783 91.59418 90.54201 assigned negative charge : -288.4263 centred at (gu) : 89.22338 91.85398 90.93426 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 51850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17018 grid for indexing accessible points = 1.400000 m= 18131 mr = 35598 m= 2339 mr = 13717 m= 79 mr = 1465 m= 0 mr = 18 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1916 time to turn everything in is 0.4100000 number of dielectric boundary points 21601 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 14307 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) : 0.6001248 object centre at (A) : 5.423500 0.3059998 17.97800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9155063E-03 -6.6799638E-03 midg,1,midg; midg,igrid,midg 6.0609505E-03 -3.7338242E-03 1,midg,midg; igrid,midg,midg 3.5563417E-02 2.7381461E-02 gauss-seidel spectral radius is 0.9983962 estimated iterations to convergence 198 setup time was (sec) 0.6900000 now iterating at: 09:08:39 rms-change max change #iterations 3.250029 147.2543 at 10iterations 1.428902 61.75772 at 20iterations 0.6283430 35.12773 at 30iterations 0.2750682 10.70178 at 40iterations 0.1205556 4.505781 at 50iterations 5.2955993E-02 1.926685 at 60iterations 2.3327233E-02 0.8554906 at 70iterations 1.0237709E-02 0.4613686 at 80iterations 4.4995490E-03 0.1897359 at 90iterations 1.9771254E-03 8.0904007E-02 at 100iterations 8.6758024E-04 3.4570694E-02 at 110iterations 3.8198425E-04 1.5963763E-02 at 120iterations finished qdiffx linear iterations at : 09:08:46 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 3.8198425E-04 1.5963763E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 09:08:47 7.649u 0.242s 0:08.28 95.1% 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 09:08:47 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.700561 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): -24.23700 35.08400 ymin,ymax (A): -19.60700 20.21900 zmin,zma (A): -2.689000 38.64500 x,y,z range (A): 59.32100 39.82600 41.33400 scale (grids/A): 2.700561 object centre (A): 5.423500 0.3059998 17.97800 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 88.82670 92.39130 90.81313 assigned negative charge : -288.4263 centred at (gu) : 88.83509 92.78103 91.40144 start vw surface at 0.1600000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 119851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17018 grid for indexing accessible points = 1.400000 m= 59807 mr = 86151 m= 20254 mr = 49466 m= 3962 mr = 16704 m= 342 mr = 2979 m= 8 mr = 186 m= 0 mr = 2 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 6542 time to turn everything in is 1.000000 number of dielectric boundary points 48736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 14653 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) : 1.800374 object centre at (A) : 5.423500 0.3059998 17.97800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9986295E-02 -6.7503534E-02 midg,1,midg; midg,igrid,midg 5.2716181E-02 -3.6632992E-02 1,midg,midg; igrid,midg,midg 0.3930165 0.2957796 gauss-seidel spectral radius is 0.9991715 estimated iterations to convergence 274 setup time was (sec) 1.310000 now iterating at: 09:08:48 rms-change max change #iterations 7.764187 246.9282 at 10iterations 4.358944 106.3433 at 20iterations 2.431201 55.50163 at 30iterations 1.349448 31.74443 at 40iterations 0.7488327 16.55729 at 50iterations 0.4154657 8.951980 at 60iterations 0.2308707 5.445395 at 70iterations 0.1284389 2.761415 at 80iterations 7.0799716E-02 1.498846 at 90iterations 3.9322134E-02 0.8967466 at 100iterations 2.1803606E-02 0.4967685 at 110iterations 1.2074074E-02 0.2601013 at 120iterations 6.6957078E-03 0.1470528 at 130iterations 3.7243001E-03 8.2031250E-02 at 140iterations 2.0639051E-03 4.8610687E-02 at 150iterations 1.1459904E-03 2.4280548E-02 at 160iterations 6.3441851E-04 1.4875412E-02 at 170iterations 3.5244733E-04 7.9574585E-03 at 180iterations finished qdiffx linear iterations at : 09:09:00 total time elapsed so far: 13.22000 # loops : 180 mean,max change (kT/e) : 3.5244733E-04 7.9574585E-03 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.41000 DelPhi exited at 09:09:01 13.410u 0.223s 0:13.92 97.9% 0+0k 0+0io 0pf+0w