Mon Oct 10 10:56:32 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 10:56:32 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5416 !!! WARNING: HIR 693 has a net charge of 0.5140 !!! WARNING: ADP 1588 has a net charge of -2.0000 !!! WARNING: ADP 1590 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5284722 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): -20.49200 46.87200 ymin,ymax (A): -28.13000 34.99900 zmin,zma (A): -19.79900 46.11700 x,y,z range (A): 67.36400 63.12900 65.91600 scale (grids/A): 0.5284722 object centre (A): 13.19000 3.434500 13.15900 number of atom coordinates read : 5416 total number of charged atoms : 5260 net assigned charge : 6.514038 assigned positive charge : 866.2494 centred at (gu) : 91.05443 89.14385 88.84518 assigned negative charge : -859.7430 centred at (gu) : 91.02544 89.12825 88.89919 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9770 nv = 96 ne = 84 npr = 107102 no. pairs analyzed = 107102 no. exposed pairs = 6632 no. arc points = 44560 no. surface atoms = 2232 nbur = 3184 mkacc time = 0.2500000 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 = 1.624000 m= 368 mr = 5407 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.5000000 number of dielectric boundary points 4724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4481 ## 596 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2993761E-10 -1.1750469E-10 midg,1,midg; midg,igrid,midg 1.1182203E-10 2.3787516E-10 1,midg,midg; igrid,midg,midg 4.7425059E-12 4.9899557E-10 gauss-seidel spectral radius is 0.9817263 estimated iterations to convergence 61 setup time was (sec) 0.7400000 now iterating at: 10:56:33 rms-change max change #iterations 8.9505516E-02 11.83243 at 10iterations 6.0171410E-03 0.7283421 at 20iterations 8.3567022E-04 0.1591721 at 30iterations 2.9331562E-04 6.1172485E-02 at 40iterations 1.1677748E-04 2.3900986E-02 at 50iterations finished qdiffx linear iterations at : 10:56:35 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.1677748E-04 2.3900986E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 10:56:36 3.435u 0.242s 0:04.01 91.5% 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 10:56:36 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5416 !!! WARNING: HIR 693 has a net charge of 0.5140 !!! WARNING: ADP 1588 has a net charge of -2.0000 !!! WARNING: ADP 1590 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.585417 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): -20.49200 46.87200 ymin,ymax (A): -28.13000 34.99900 zmin,zma (A): -19.79900 46.11700 x,y,z range (A): 67.36400 63.12900 65.91600 scale (grids/A): 1.585417 object centre (A): 13.19000 3.434500 13.15900 number of atom coordinates read : 5416 total number of charged atoms : 5260 net assigned charge : 6.514038 assigned positive charge : 866.2494 centred at (gu) : 93.16167 87.43050 86.53394 assigned negative charge : -859.7430 centred at (gu) : 93.07653 87.38490 86.69765 start vw surface at 0.2500000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 110650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 35075 mr = 79160 m= 3206 mr = 24397 m= 76 mr = 1467 m= 0 mr = 4 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 499 time to turn everything in is 0.8500000 number of dielectric boundary points 43979 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 597 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 39945 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) : 0.5284722 object centre at (A) : 13.19000 3.434500 13.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6838327E-03 -3.9107442E-02 midg,1,midg; midg,igrid,midg 1.3456058E-03 3.2003998E-04 1,midg,midg; igrid,midg,midg 2.7951453E-02 1.6061299E-02 gauss-seidel spectral radius is 0.9982978 estimated iterations to convergence 192 setup time was (sec) 1.140000 now iterating at: 10:56:37 rms-change max change #iterations 4.621825 250.8336 at 10iterations 1.982219 63.48316 at 20iterations 0.8512456 25.65976 at 30iterations 0.3653039 10.38391 at 40iterations 0.1566816 5.104370 at 50iterations 6.7423850E-02 1.964293 at 60iterations 2.9066777E-02 0.9756794 at 70iterations 1.2576794E-02 0.3626614 at 80iterations 5.4932851E-03 0.1707792 at 90iterations 2.4451436E-03 8.1958771E-02 at 100iterations 1.1417539E-03 3.8330078E-02 at 110iterations 5.8017886E-04 2.0050049E-02 at 120iterations finished qdiffx linear iterations at : 10:56:44 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 5.8017886E-04 2.0050049E-02 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 10:56:44 8.045u 0.217s 0:08.58 96.1% 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 10:56:44 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5416 !!! WARNING: HIR 693 has a net charge of 0.5140 !!! WARNING: ADP 1588 has a net charge of -2.0000 !!! WARNING: ADP 1590 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.378125 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): -20.49200 46.87200 ymin,ymax (A): -28.13000 34.99900 zmin,zma (A): -19.79900 46.11700 x,y,z range (A): 67.36400 63.12900 65.91600 scale (grids/A): 2.378125 object centre (A): 13.19000 3.434500 13.15900 number of atom coordinates read : 5416 total number of charged atoms : 5260 net assigned charge : 6.514038 assigned positive charge : 866.2494 centred at (gu) : 94.74207 86.14546 84.80029 assigned negative charge : -859.7430 centred at (gu) : 94.61500 86.07721 85.04639 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 257900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44560 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 123611 mr = 193482 m= 33173 mr = 99422 m= 4698 mr = 24561 m= 268 mr = 2869 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 1655 time to turn everything in is 1.830000 number of dielectric boundary points 99218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 42019 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) : 1.585417 object centre at (A) : 13.19000 3.434500 13.15900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2786621E-02 -1.011069 midg,1,midg; midg,igrid,midg -4.9437348E-02 -1.1174152E-02 1,midg,midg; igrid,midg,midg 0.5950424 0.2023695 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.160000 now iterating at: 10:56:47 rms-change max change #iterations 12.08157 335.4181 at 10iterations 7.061867 154.6158 at 20iterations 4.099514 86.94386 at 30iterations 2.363625 43.32804 at 40iterations 1.357493 27.39999 at 50iterations 0.7775091 14.37809 at 60iterations 0.4444332 7.579291 at 70iterations 0.2537241 4.502480 at 80iterations 0.1446351 2.609543 at 90iterations 8.2286142E-02 1.358821 at 100iterations 4.6793222E-02 0.8111115 at 110iterations 2.6641008E-02 0.4238376 at 120iterations 1.5153810E-02 0.2636375 at 130iterations 8.6321188E-03 0.1446152 at 140iterations 4.9487376E-03 8.7591663E-02 at 150iterations 2.8533193E-03 5.0563812E-02 at 160iterations 1.6664700E-03 3.5127640E-02 at 170iterations 1.0053909E-03 1.8539429E-02 at 180iterations finished qdiffx linear iterations at : 10:56:59 total time elapsed so far: 13.84000 # loops : 180 mean,max change (kT/e) : 1.0053909E-03 1.8539429E-02 energy calculations done at 13.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 10:56:59 14.009u 0.277s 0:14.61 97.6% 0+0k 0+0io 0pf+0w