Mon Oct 10 16:59:33 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+sph.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 = amb.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 16:59:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1767 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7241365 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): -56.34200 -7.180000 ymin,ymax (A): 1.300000 47.19500 zmin,zma (A): -44.28300 2.289000 x,y,z range (A): 49.16200 45.89500 46.57200 scale (grids/A): 0.7241365 object centre (A): -31.76100 24.24750 -20.99700 number of atom coordinates read : 1767 total number of charged atoms : 1639 net assigned charge : -1.499987 assigned positive charge : 251.0244 centred at (gu) : 88.35505 89.96202 89.43320 assigned negative charge : -252.5243 centred at (gu) : 88.11770 90.10950 89.44444 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6370 nv = 96 ne = 84 npr = 37252 no. pairs analyzed = 37252 no. exposed pairs = 2239 no. arc points = 16162 no. surface atoms = 756 nbur = 1011 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 401 mr = 3434 m= 2 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.1600000 number of dielectric boundary points 3256 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1287 ## 106 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6772 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0397180E-08 -2.0100822E-08 midg,1,midg; midg,igrid,midg 6.8059862E-08 -1.0098336E-07 1,midg,midg; igrid,midg,midg -2.1455749E-07 8.5012296E-08 gauss-seidel spectral radius is 0.9900334 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 16:59:34 rms-change max change #iterations 0.2012568 33.68634 at 10iterations 2.5629619E-02 4.067158 at 20iterations 3.2532206E-03 0.4623680 at 30iterations 4.2079933E-04 5.8269501E-02 at 40iterations 5.3571228E-05 8.7211132E-03 at 50iterations finished qdiffx linear iterations at : 16:59:37 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 5.3571228E-05 8.7211132E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 16:59:38 3.388u 0.174s 0:04.11 86.3% 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 16:59:38 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1767 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: 2.172410 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): -56.34200 -7.180000 ymin,ymax (A): 1.300000 47.19500 zmin,zma (A): -44.28300 2.289000 x,y,z range (A): 49.16200 45.89500 46.57200 scale (grids/A): 2.172410 object centre (A): -31.76100 24.24750 -20.99700 number of atom coordinates read : 1767 total number of charged atoms : 1639 net assigned charge : -1.499987 assigned positive charge : 251.0244 centred at (gu) : 85.06536 89.88631 88.29985 assigned negative charge : -252.5243 centred at (gu) : 84.35326 90.32890 88.33355 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 66735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16162 grid for indexing accessible points = 1.400000 m= 25274 mr = 44962 m= 5086 mr = 19074 m= 509 mr = 3478 m= 14 mr = 321 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2972 time to turn everything in is 0.3600000 number of dielectric boundary points 29781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 13057 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) : 0.7241365 object centre at (A) : -31.76100 24.24750 -20.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9812109E-03 4.0834013E-02 midg,1,midg; midg,igrid,midg -3.6487170E-02 -6.5106720E-02 1,midg,midg; igrid,midg,midg -3.3677347E-02 4.6461437E-02 gauss-seidel spectral radius is 0.9988613 estimated iterations to convergence 235 setup time was (sec) 0.5900000 now iterating at: 16:59:38 rms-change max change #iterations 4.254022 209.4769 at 10iterations 2.120211 79.68150 at 20iterations 1.053669 35.95049 at 30iterations 0.5267803 18.63007 at 40iterations 0.2636261 7.789009 at 50iterations 0.1314840 4.112549 at 60iterations 6.5733321E-02 2.382246 at 70iterations 3.2900635E-02 1.007507 at 80iterations 1.6361814E-02 0.5349770 at 90iterations 8.1975637E-03 0.2645702 at 100iterations 4.1088043E-03 0.1341877 at 110iterations 2.0473257E-03 6.3041687E-02 at 120iterations finished qdiffx linear iterations at : 16:59:45 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 2.0473257E-03 6.3041687E-02 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 16:59:46 7.884u 0.172s 0:08.76 91.8% 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 16:59:46 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1767 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.258614 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): -56.34200 -7.180000 ymin,ymax (A): 1.300000 47.19500 zmin,zma (A): -44.28300 2.289000 x,y,z range (A): 49.16200 45.89500 46.57200 scale (grids/A): 3.258614 object centre (A): -31.76100 24.24750 -20.99700 number of atom coordinates read : 1767 total number of charged atoms : 1639 net assigned charge : -1.499987 assigned positive charge : 251.0244 centred at (gu) : 82.59805 89.82964 87.44984 assigned negative charge : -252.5243 centred at (gu) : 81.52993 90.49336 87.50033 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 153752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16162 grid for indexing accessible points = 1.400000 m= 78609 mr = 108881 m= 32113 mr = 64335 m= 9467 mr = 26468 m= 2081 mr = 7545 m= 314 mr = 1675 m= 19 mr = 221 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 9549 time to turn everything in is 1.040000 number of dielectric boundary points 67231 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 13112 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) : 2.172410 object centre at (A) : -31.76100 24.24750 -20.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9823441E-02 0.4948045 midg,1,midg; midg,igrid,midg -0.4907490 -0.4366671 1,midg,midg; igrid,midg,midg -0.1146746 0.4361108 gauss-seidel spectral radius is 0.9993098 estimated iterations to convergence 300 setup time was (sec) 1.260000 now iterating at: 16:59:48 rms-change max change #iterations 9.401764 396.2706 at 10iterations 5.534529 113.0580 at 20iterations 3.262451 68.32272 at 30iterations 1.912119 45.14504 at 40iterations 1.124100 20.36239 at 50iterations 0.6571360 12.35861 at 60iterations 0.3846127 7.089966 at 70iterations 0.2249190 4.236073 at 80iterations 0.1315690 2.350144 at 90iterations 7.6938726E-02 1.295545 at 100iterations 4.5035109E-02 0.8511467 at 110iterations 2.6371267E-02 0.4825497 at 120iterations 1.5411049E-02 0.2779541 at 130iterations 9.0384660E-03 0.1559601 at 140iterations 5.2794805E-03 9.9364102E-02 at 150iterations 3.1010476E-03 5.5877686E-02 at 160iterations 1.8139686E-03 3.3580065E-02 at 170iterations 1.0645131E-03 1.7993927E-02 at 180iterations finished qdiffx linear iterations at : 16:59:59 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 1.0645131E-03 1.7993927E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 17:00:00 12.637u 0.236s 0:13.48 95.4% 0+0k 0+0io 0pf+0w