Mon Oct 10 14:25:38 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 14:25:38 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 0.6213782 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): -7.656000 44.57200 ymin,ymax (A): 3.547000 60.83900 zmin,zma (A): -14.75500 36.88800 x,y,z range (A): 52.22800 57.29200 51.64300 scale (grids/A): 0.6213782 object centre (A): 18.45800 32.19300 11.06650 number of atom coordinates read : 2461 total number of charged atoms : 2303 net assigned charge : -3.999990 assigned positive charge : 363.1081 centred at (gu) : 89.99611 89.18759 90.06892 assigned negative charge : -367.1084 centred at (gu) : 89.76932 89.22636 90.10374 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6504 nv = 96 ne = 84 npr = 48892 no. pairs analyzed = 48892 no. exposed pairs = 3346 no. arc points = 23644 no. surface atoms = 1128 nbur = 1333 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3335 m= 3 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2215 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0747334E-09 -5.7318648E-09 midg,1,midg; midg,igrid,midg -9.6158248E-10 -4.9541398E-09 1,midg,midg; igrid,midg,midg -1.8599403E-08 1.1101200E-08 gauss-seidel spectral radius is 0.9865848 estimated iterations to convergence 71 setup time was (sec) 0.7100000 now iterating at: 14:25:39 rms-change max change #iterations 0.1235017 17.72751 at 10iterations 1.1311878E-02 1.693447 at 20iterations 1.0426114E-03 0.1736422 at 30iterations 9.6118063E-05 1.4377594E-02 at 40iterations 8.8651859E-06 1.2283325E-03 at 50iterations finished qdiffx linear iterations at : 14:25:43 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 8.8651859E-06 1.2283325E-03 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 14:25:44 4.441u 0.414s 0:05.19 93.4% 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 Mon Oct 10 2011 at 14:25:44 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 1.864135 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): -7.656000 44.57200 ymin,ymax (A): 3.547000 60.83900 zmin,zma (A): -14.75500 36.88800 x,y,z range (A): 52.22800 57.29200 51.64300 scale (grids/A): 1.864135 object centre (A): 18.45800 32.19300 11.06650 number of atom coordinates read : 2461 total number of charged atoms : 2303 net assigned charge : -3.999990 assigned positive charge : 363.1081 centred at (gu) : 89.98775 87.56233 90.20637 assigned negative charge : -367.1084 centred at (gu) : 89.30768 87.67884 90.31104 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23644 grid for indexing accessible points = 1.400000 m= 24582 mr = 47132 m= 3535 mr = 17438 m= 178 mr = 1839 m= 2 mr = 44 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.7300000 number of dielectric boundary points 32098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 18076 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) : 0.6213782 object centre at (A) : 18.45800 32.19300 11.06650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2219613E-03 -1.5834840E-02 midg,1,midg; midg,igrid,midg -1.3299419E-02 1.7459303E-04 1,midg,midg; igrid,midg,midg -3.8172867E-02 6.9257864E-03 gauss-seidel spectral radius is 0.9985720 estimated iterations to convergence 210 setup time was (sec) 1.060000 now iterating at: 14:25:45 rms-change max change #iterations 3.944688 178.1007 at 10iterations 1.807971 62.42666 at 20iterations 0.8265418 30.77088 at 30iterations 0.3806759 12.62191 at 40iterations 0.1744701 6.067966 at 50iterations 8.0276608E-02 2.588937 at 60iterations 3.6945708E-02 1.289558 at 70iterations 1.6988724E-02 0.5626073 at 80iterations 7.8059919E-03 0.2499561 at 90iterations 3.5905023E-03 0.1265197 at 100iterations 1.6516638E-03 5.4667473E-02 at 110iterations 7.6056941E-04 2.5904655E-02 at 120iterations finished qdiffx linear iterations at : 14:25:54 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 7.6056941E-04 2.5904655E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.25000 DelPhi exited at 14:25:55 10.255u 0.471s 0:11.22 95.5% 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 14:25:55 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2461 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: 2.796202 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): -7.656000 44.57200 ymin,ymax (A): 3.547000 60.83900 zmin,zma (A): -14.75500 36.88800 x,y,z range (A): 52.22800 57.29200 51.64300 scale (grids/A): 2.796202 object centre (A): 18.45800 32.19300 11.06650 number of atom coordinates read : 2461 total number of charged atoms : 2303 net assigned charge : -3.999990 assigned positive charge : 363.1081 centred at (gu) : 89.98154 86.34344 90.30945 assigned negative charge : -367.1084 centred at (gu) : 88.96153 86.51818 90.46646 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 162208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23644 grid for indexing accessible points = 1.400000 m= 80423 mr = 114602 m= 27887 mr = 64368 m= 5896 mr = 21467 m= 715 mr = 3899 m= 52 mr = 373 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 1.910000 number of dielectric boundary points 72449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 18421 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) : 1.864135 object centre at (A) : 18.45800 32.19300 11.06650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2175895E-02 -0.2441089 midg,1,midg; midg,igrid,midg -0.2001737 5.9452545E-02 1,midg,midg; igrid,midg,midg -0.3676843 3.2666001E-02 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 2.280000 now iterating at: 14:25:58 rms-change max change #iterations 9.494144 290.3049 at 10iterations 5.592865 143.8660 at 20iterations 3.262317 95.90345 at 30iterations 1.894153 42.98331 at 40iterations 1.095460 25.29749 at 50iterations 0.6323483 13.65072 at 60iterations 0.3646394 7.922357 at 70iterations 0.2095146 4.389966 at 80iterations 0.1202950 2.348057 at 90iterations 6.9198042E-02 1.382523 at 100iterations 3.9671659E-02 0.8013573 at 110iterations 2.2726590E-02 0.4418020 at 120iterations 1.2992803E-02 0.2853241 at 130iterations 7.4398578E-03 0.1672516 at 140iterations 4.2724498E-03 9.7350597E-02 at 150iterations 2.4421411E-03 5.1116943E-02 at 160iterations 1.3987813E-03 3.0649185E-02 at 170iterations 8.0103253E-04 1.5365601E-02 at 180iterations finished qdiffx linear iterations at : 14:26:13 total time elapsed so far: 17.59000 # loops : 180 mean,max change (kT/e) : 8.0103253E-04 1.5365601E-02 energy calculations done at 17.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.80000 DelPhi exited at 14:26:14 17.804u 0.489s 0:19.47 93.8% 0+0k 0+0io 0pf+0w