Sat Oct 8 21:56:02 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 Sat Oct 8 2011 at 21:56:02 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4813022 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): -82.39700 -8.431001 ymin,ymax (A): -28.11900 43.18300 zmin,zma (A): -53.82700 13.72900 x,y,z range (A): 73.96600 71.30200 67.55600 scale (grids/A): 0.4813022 object centre (A): -45.41400 7.532000 -20.04900 number of atom coordinates read : 4299 total number of charged atoms : 4131 net assigned charge : 11.50005 assigned positive charge : 659.9974 centred at (gu) : 90.33590 92.32892 90.48482 assigned negative charge : -648.5006 centred at (gu) : 90.33170 92.31222 90.48269 start vw surface at 0.2000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6355 nv = 96 ne = 84 npr = 82639 no. pairs analyzed = 82639 no. exposed pairs = 5916 no. arc points = 41929 no. surface atoms = 1971 nbur = 2328 mkacc time = 0.2000000 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 = 1.792000 m= 221 mr = 2898 m= 0 mr = 7 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4014 ## 720 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 8596 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4152181E-11 4.7409757E-11 midg,1,midg; midg,igrid,midg 1.6183383E-11 9.6356589E-11 1,midg,midg; igrid,midg,midg 3.4378583E-11 4.6936191E-11 gauss-seidel spectral radius is 0.9779177 estimated iterations to convergence 56 setup time was (sec) 0.7300000 now iterating at: 21:56:03 rms-change max change #iterations 4.6911649E-02 8.739101 at 10iterations 2.4250818E-03 0.4478531 at 20iterations 2.5823311E-04 4.2217255E-02 at 30iterations 6.1840619E-05 1.2487411E-02 at 40iterations 1.6325881E-05 3.4055710E-03 at 50iterations finished qdiffx linear iterations at : 21:56:06 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 1.6325881E-05 3.4055710E-03 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 21:56:07 4.344u 0.242s 0:04.87 94.0% 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 Sat Oct 8 2011 at 21:56:07 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.443907 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): -82.39700 -8.431001 ymin,ymax (A): -28.11900 43.18300 zmin,zma (A): -53.82700 13.72900 x,y,z range (A): 73.96600 71.30200 67.55600 scale (grids/A): 1.443907 object centre (A): -45.41400 7.532000 -20.04900 number of atom coordinates read : 4299 total number of charged atoms : 4131 net assigned charge : 11.50005 assigned positive charge : 659.9974 centred at (gu) : 91.00673 96.98556 91.45346 assigned negative charge : -648.5006 centred at (gu) : 90.99466 96.93626 91.44773 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41929 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 18765 mr = 46536 m= 1390 mr = 10907 m= 18 mr = 445 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 34471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 640 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 30288 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) : 0.4813022 object centre at (A) : -45.41400 7.532000 -20.04900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4095924E-03 1.0901888E-02 midg,1,midg; midg,igrid,midg 3.0338678E-03 4.7680065E-03 1,midg,midg; igrid,midg,midg 7.8074327E-03 1.4920022E-02 gauss-seidel spectral radius is 0.9977923 estimated iterations to convergence 169 setup time was (sec) 0.9100000 now iterating at: 21:56:08 rms-change max change #iterations 3.090200 127.4936 at 10iterations 1.175637 48.84621 at 20iterations 0.4468141 19.07356 at 30iterations 0.1697197 6.350767 at 40iterations 6.4869314E-02 2.721194 at 50iterations 2.4652217E-02 0.9254913 at 60iterations 9.4492594E-03 0.3512335 at 70iterations 3.6260162E-03 0.1360947 at 80iterations 1.3993625E-03 5.3911209E-02 at 90iterations 5.5380020E-04 2.2655487E-02 at 100iterations 2.3087456E-04 9.7818375E-03 at 110iterations 1.0433850E-04 4.4240952E-03 at 120iterations finished qdiffx linear iterations at : 21:56:16 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 1.0433850E-04 4.4240952E-03 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.670000 DelPhi exited at 21:56:17 9.672u 0.262s 0:10.23 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 Sat Oct 8 2011 at 21:56:17 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4299 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.165860 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): -82.39700 -8.431001 ymin,ymax (A): -28.11900 43.18300 zmin,zma (A): -53.82700 13.72900 x,y,z range (A): 73.96600 71.30200 67.55600 scale (grids/A): 2.165860 object centre (A): -45.41400 7.532000 -20.04900 number of atom coordinates read : 4299 total number of charged atoms : 4131 net assigned charge : 11.50005 assigned positive charge : 659.9974 centred at (gu) : 91.50978 100.4782 92.17987 assigned negative charge : -648.5006 centred at (gu) : 91.49186 100.4044 92.17147 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 168574 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41929 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 68946 mr = 115650 m= 15049 mr = 50289 m= 1820 mr = 9492 m= 59 mr = 949 m= 0 mr = 7 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 78061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 32868 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) : 1.443907 object centre at (A) : -45.41400 7.532000 -20.04900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0564085E-02 0.3138897 midg,1,midg; midg,igrid,midg 4.5863498E-02 0.1303874 1,midg,midg; igrid,midg,midg 0.1944790 0.4671374 gauss-seidel spectral radius is 0.9990426 estimated iterations to convergence 255 setup time was (sec) 1.840000 now iterating at: 21:56:19 rms-change max change #iterations 8.905046 282.3184 at 10iterations 4.944903 159.4216 at 20iterations 2.726725 82.40353 at 30iterations 1.490719 41.13829 at 40iterations 0.8116581 18.35024 at 50iterations 0.4395652 9.765031 at 60iterations 0.2367318 6.345398 at 70iterations 0.1275623 3.020267 at 80iterations 6.8459958E-02 1.526093 at 90iterations 3.6746375E-02 0.8632050 at 100iterations 1.9667920E-02 0.3992767 at 110iterations 1.0513673E-02 0.2178787 at 120iterations 5.6130891E-03 0.1196671 at 130iterations 2.9951436E-03 6.3949585E-02 at 140iterations 1.5990618E-03 3.3150673E-02 at 150iterations 8.5236615E-04 1.9336700E-02 at 160iterations 4.5456830E-04 9.8114014E-03 at 170iterations 2.4238984E-04 5.2719116E-03 at 180iterations finished qdiffx linear iterations at : 21:56:34 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 2.4238984E-04 5.2719116E-03 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.38000 DelPhi exited at 21:56:34 16.382u 0.349s 0:17.02 98.2% 0+0k 0+0io 0pf+0w