Sun Oct 9 01:48:53 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 Sun Oct 9 2011 at 01:48:53 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3384 !!! WARNING: HIT 83 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 0.5479790 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): -40.74200 15.83100 ymin,ymax (A): -50.00600 12.65300 zmin,zma (A): -13.36700 51.59900 x,y,z range (A): 56.57300 62.65900 64.96600 scale (grids/A): 0.5479790 object centre (A): -12.45550 -18.67650 19.11600 number of atom coordinates read : 3384 total number of charged atoms : 3243 net assigned charge : 14.47102 assigned positive charge : 505.9105 centred at (gu) : 90.05418 89.24438 88.67241 assigned negative charge : -491.4413 centred at (gu) : 90.17336 89.28328 88.50951 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6838 nv = 96 ne = 84 npr = 65507 no. pairs analyzed = 65507 no. exposed pairs = 4512 no. arc points = 33062 no. surface atoms = 1497 nbur = 1887 mkacc time = 0.1100000 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 = 1.568000 m= 261 mr = 3369 m= 0 mr = 13 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2400000 number of dielectric boundary points 3717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3459 ## 504 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9037 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7182130E-10 1.6280876E-09 midg,1,midg; midg,igrid,midg 1.5578570E-09 5.7205579E-10 1,midg,midg; igrid,midg,midg 1.8921922E-09 3.5794687E-11 gauss-seidel spectral radius is 0.9828752 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 01:48:54 rms-change max change #iterations 8.0592453E-02 13.95902 at 10iterations 5.4111797E-03 0.9025936 at 20iterations 3.8089004E-04 5.2253723E-02 at 30iterations 3.4200490E-05 4.5471191E-03 at 40iterations 4.6773193E-06 5.0163269E-04 at 50iterations finished qdiffx linear iterations at : 01:48:57 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 4.6773193E-06 5.0163269E-04 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 01:48:58 3.753u 0.213s 0:04.53 87.4% 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 Sun Oct 9 2011 at 01:48:58 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3384 !!! WARNING: HIT 83 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.643937 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): -40.74200 15.83100 ymin,ymax (A): -50.00600 12.65300 zmin,zma (A): -13.36700 51.59900 x,y,z range (A): 56.57300 62.65900 64.96600 scale (grids/A): 1.643937 object centre (A): -12.45550 -18.67650 19.11600 number of atom coordinates read : 3384 total number of charged atoms : 3243 net assigned charge : 14.47102 assigned positive charge : 505.9105 centred at (gu) : 90.16148 87.73215 86.01618 assigned negative charge : -491.4413 centred at (gu) : 90.51992 87.84948 85.52832 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33062 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 22862 mr = 50380 m= 2368 mr = 15222 m= 64 mr = 1112 m= 0 mr = 8 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1865 time to turn everything in is 0.3800000 number of dielectric boundary points 34674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 397 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24921 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) : 0.5479790 object centre at (A) : -12.45550 -18.67650 19.11600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8197265E-03 3.0544005E-02 midg,1,midg; midg,igrid,midg 3.6196429E-02 2.7442886E-02 1,midg,midg; igrid,midg,midg 1.0670437E-02 -4.7438629E-03 gauss-seidel spectral radius is 0.9982730 estimated iterations to convergence 191 setup time was (sec) 0.6400000 now iterating at: 01:48:59 rms-change max change #iterations 3.620468 159.3810 at 10iterations 1.534773 55.16010 at 20iterations 0.6508522 23.53265 at 30iterations 0.2765528 8.961966 at 40iterations 0.1174392 4.060601 at 50iterations 4.9860191E-02 1.597061 at 60iterations 2.1224836E-02 0.7996054 at 70iterations 9.0301000E-03 0.2981272 at 80iterations 3.8635228E-03 0.1305313 at 90iterations 1.6457204E-03 5.6997299E-02 at 100iterations 7.0106931E-04 2.4180889E-02 at 110iterations 2.9867276E-04 1.0293007E-02 at 120iterations finished qdiffx linear iterations at : 01:49:07 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 2.9867276E-04 1.0293007E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.790000 DelPhi exited at 01:49:07 8.791u 0.250s 0:09.31 97.0% 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 Sun Oct 9 2011 at 01:49:07 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3384 !!! WARNING: HIT 83 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -0.0020 !!! WARNING: TPO 2 has a net charge of -1.5410 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: 2.465905 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): -40.74200 15.83100 ymin,ymax (A): -50.00600 12.65300 zmin,zma (A): -13.36700 51.59900 x,y,z range (A): 56.57300 62.65900 64.96600 scale (grids/A): 2.465905 object centre (A): -12.45550 -18.67650 19.11600 number of atom coordinates read : 3384 total number of charged atoms : 3243 net assigned charge : 14.47102 assigned positive charge : 505.9105 centred at (gu) : 90.24193 86.59799 84.02406 assigned negative charge : -491.4413 centred at (gu) : 90.77959 86.77425 83.29237 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 176744 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33062 grid for indexing accessible points = 1.400000 m= 78675 mr = 123382 m= 22202 mr = 60998 m= 3689 mr = 16475 m= 296 mr = 2360 m= 3 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 6436 time to turn everything in is 0.9500000 number of dielectric boundary points 78229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 25922 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) : 1.643937 object centre at (A) : -12.45550 -18.67650 19.11600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3613371E-02 0.4951486 midg,1,midg; midg,igrid,midg 0.5915639 0.5842991 1,midg,midg; igrid,midg,midg 0.1477876 -2.4487741E-02 gauss-seidel spectral radius is 0.9991847 estimated iterations to convergence 277 setup time was (sec) 1.260000 now iterating at: 01:49:09 rms-change max change #iterations 9.359639 340.7764 at 10iterations 5.387748 141.8365 at 20iterations 3.076229 73.72475 at 30iterations 1.743225 37.73489 at 40iterations 0.9839885 23.73879 at 50iterations 0.5553809 12.42070 at 60iterations 0.3113254 6.275138 at 70iterations 0.1748845 3.346307 at 80iterations 9.8082043E-02 1.859520 at 90iterations 5.4876231E-02 1.025923 at 100iterations 3.0747250E-02 0.6103935 at 110iterations 1.7168369E-02 0.3639717 at 120iterations 9.6013034E-03 0.1885910 at 130iterations 5.3565763E-03 0.1030053 at 140iterations 2.9977565E-03 5.5332184E-02 at 150iterations 1.6748096E-03 3.8331032E-02 at 160iterations 9.3538302E-04 1.7732382E-02 at 170iterations 5.2265183E-04 9.6187592E-03 at 180iterations finished qdiffx linear iterations at : 01:49:23 total time elapsed so far: 15.33000 # loops : 180 mean,max change (kT/e) : 5.2265183E-04 9.6187592E-03 energy calculations done at 15.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.47000 DelPhi exited at 01:49:23 15.468u 0.275s 0:16.02 98.1% 0+0k 0+0io 0pf+0w