Mon Oct 10 23:39:24 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 23:39:24 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 !!! WARNING: GLM 42 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5533707 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): -24.49100 26.07100 ymin,ymax (A): -33.63100 22.15900 zmin,zma (A): -6.994000 57.33900 x,y,z range (A): 50.56200 55.79000 64.33300 scale (grids/A): 0.5533707 object centre (A): 0.7900000 -5.735998 25.17250 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.9060056 assigned positive charge : 419.3172 centred at (gu) : 91.42754 89.41404 91.10255 assigned negative charge : -418.4125 centred at (gu) : 91.29816 89.48962 91.01997 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5848 nv = 96 ne = 84 npr = 54612 no. pairs analyzed = 54612 no. exposed pairs = 3914 no. arc points = 27823 no. surface atoms = 1308 nbur = 1516 mkacc time = 0.1200000 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= 256 mr = 2814 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2871 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8404486E-10 9.4225827E-10 midg,1,midg; midg,igrid,midg 7.6313217E-10 -4.9967530E-10 1,midg,midg; igrid,midg,midg -7.2345069E-10 1.5565196E-09 gauss-seidel spectral radius is 0.9831607 estimated iterations to convergence 63 setup time was (sec) 0.5400000 now iterating at: 23:39:25 rms-change max change #iterations 7.4199781E-02 12.86102 at 10iterations 5.0960798E-03 1.179749 at 20iterations 4.0489758E-04 6.4271927E-02 at 30iterations 4.9861494E-05 7.4424744E-03 at 40iterations 9.6460044E-06 1.2302399E-03 at 50iterations finished qdiffx linear iterations at : 23:39:27 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 9.6460044E-06 1.2302399E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 23:39:28 3.296u 0.178s 0:03.88 89.1% 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 23:39:28 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 !!! WARNING: GLM 42 has a net charge of -0.0940 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: 1.660112 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): -24.49100 26.07100 ymin,ymax (A): -33.63100 22.15900 zmin,zma (A): -6.994000 57.33900 x,y,z range (A): 50.56200 55.79000 64.33300 scale (grids/A): 1.660112 object centre (A): 0.7900000 -5.735998 25.17250 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.9060056 assigned positive charge : 419.3172 centred at (gu) : 94.28175 88.24133 93.30701 assigned negative charge : -418.4125 centred at (gu) : 93.89426 88.46881 93.05953 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19871 mr = 41481 m= 2226 mr = 13269 m= 63 mr = 1128 m= 0 mr = 10 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 30337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 305 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21160 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) : 0.5533707 object centre at (A) : 0.7900000 -5.735998 25.17250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2034984E-02 5.8224187E-03 midg,1,midg; midg,igrid,midg -1.4806290E-04 -9.9982191E-03 1,midg,midg; igrid,midg,midg -5.0186715E-03 2.0020336E-02 gauss-seidel spectral radius is 0.9982480 estimated iterations to convergence 190 setup time was (sec) 0.7600000 now iterating at: 23:39:29 rms-change max change #iterations 3.291540 145.9674 at 10iterations 1.385673 55.68388 at 20iterations 0.5857917 25.15691 at 30iterations 0.2471507 8.940618 at 40iterations 0.1045791 3.843192 at 50iterations 4.4100251E-02 1.654724 at 60iterations 1.8709525E-02 0.7168954 at 70iterations 7.9006189E-03 0.2918692 at 80iterations 3.3539396E-03 0.1204262 at 90iterations 1.4167520E-03 5.7887077E-02 at 100iterations 6.0423627E-04 1.9884109E-02 at 110iterations 2.6022657E-04 9.1495514E-03 at 120iterations finished qdiffx linear iterations at : 23:39:35 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 2.6022657E-04 9.1495514E-03 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 23:39:36 7.586u 0.268s 0:08.18 95.8% 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 23:39:36 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2824 !!! WARNING: GLM 42 has a net charge of -0.0940 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: 2.490168 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): -24.49100 26.07100 ymin,ymax (A): -33.63100 22.15900 zmin,zma (A): -6.994000 57.33900 x,y,z range (A): 50.56200 55.79000 64.33300 scale (grids/A): 2.490168 object centre (A): 0.7900000 -5.735998 25.17250 number of atom coordinates read : 2824 total number of charged atoms : 2738 net assigned charge : 0.9060056 assigned positive charge : 419.3172 centred at (gu) : 96.42258 87.36189 94.96048 assigned negative charge : -418.4125 centred at (gu) : 95.84137 87.70326 94.58923 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 148837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27823 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67509 mr = 102327 m= 20452 mr = 52219 m= 3456 mr = 15124 m= 245 mr = 2241 m= 11 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.090000 number of dielectric boundary points 68485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 21883 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) : 1.660112 object centre at (A) : 0.7900000 -5.735998 25.17250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5601733 0.1292403 midg,1,midg; midg,igrid,midg -5.0635420E-02 -0.1531053 1,midg,midg; igrid,midg,midg -0.1093682 0.2624205 gauss-seidel spectral radius is 0.9991646 estimated iterations to convergence 273 setup time was (sec) 1.400000 now iterating at: 23:39:38 rms-change max change #iterations 8.601062 379.4758 at 10iterations 4.891709 131.0440 at 20iterations 2.767576 62.26193 at 30iterations 1.564753 38.18974 at 40iterations 0.8788027 20.82011 at 50iterations 0.4913465 10.44977 at 60iterations 0.2738979 6.356646 at 70iterations 0.1531732 3.357828 at 80iterations 8.5319608E-02 1.988838 at 90iterations 4.7490317E-02 1.092886 at 100iterations 2.6402049E-02 0.5168228 at 110iterations 1.4690137E-02 0.3118877 at 120iterations 8.1558414E-03 0.1630859 at 130iterations 4.5337738E-03 9.7362518E-02 at 140iterations 2.5156268E-03 5.8441162E-02 at 150iterations 1.4008755E-03 3.4639597E-02 at 160iterations 7.8024605E-04 1.6273499E-02 at 170iterations 4.3622669E-04 9.1660023E-03 at 180iterations finished qdiffx linear iterations at : 23:39:48 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 4.3622669E-04 9.1660023E-03 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.02000 DelPhi exited at 23:39:49 12.026u 0.265s 0:12.73 96.4% 0+0k 0+0io 0pf+0w