Wed Dec 21 14:21:19 PST 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 Wed Dec 21 2011 at 14:21:22 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 = 1954 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6477438 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): -3.661000 48.75500 ymin,ymax (A): -5.272000 34.55000 zmin,zma (A): -23.80700 31.15300 x,y,z range (A): 52.41600 39.82200 54.96000 scale (grids/A): 0.6477438 object centre (A): 22.54700 14.63900 3.673000 number of atom coordinates read : 1954 total number of charged atoms : 1822 net assigned charge : 4.000004 assigned positive charge : 286.9621 centred at (gu) : 92.32911 89.52699 90.00338 assigned negative charge : -282.9623 centred at (gu) : 92.44989 89.41830 89.94121 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5618 nv = 96 ne = 84 npr = 40223 no. pairs analyzed = 40223 no. exposed pairs = 2536 no. arc points = 17576 no. surface atoms = 862 nbur = 1092 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3101 m= 1 mr = 34 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 0.2800000 number of dielectric boundary points 2766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1782 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6595 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1059839E-09 1.4052378E-08 midg,1,midg; midg,igrid,midg -4.2817505E-09 1.7011427E-08 1,midg,midg; igrid,midg,midg 1.2316216E-08 -8.8615417E-09 gauss-seidel spectral radius is 0.9875938 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:21:22 rms-change max change #iterations 0.1298181 22.14939 at 10iterations 1.2794775E-02 2.045014 at 20iterations 1.3172965E-03 0.1998520 at 30iterations 1.3513806E-04 2.2979736E-02 at 40iterations 1.3756296E-05 2.0904541E-03 at 50iterations finished qdiffx linear iterations at : 14:21:27 total time elapsed so far: 4.950000 # loops : 50 mean,max change (kT/e) : 1.3756296E-05 2.0904541E-03 energy calculations done at 4.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.150000 DelPhi exited at 14:21:30 5.152u 0.341s 0:08.75 62.7% 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 Wed Dec 21 2011 at 14:21:32 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.943231 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): -3.661000 48.75500 ymin,ymax (A): -5.272000 34.55000 zmin,zma (A): -23.80700 31.15300 x,y,z range (A): 52.41600 39.82200 54.96000 scale (grids/A): 1.943231 object centre (A): 22.54700 14.63900 3.673000 number of atom coordinates read : 1954 total number of charged atoms : 1822 net assigned charge : 4.000004 assigned positive charge : 286.9621 centred at (gu) : 96.98732 88.58092 90.01007 assigned negative charge : -282.9623 centred at (gu) : 97.34958 88.25518 89.82387 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60150 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17576 grid for indexing accessible points = 1.400000 m= 21640 mr = 41041 m= 3141 mr = 16296 m= 145 mr = 1980 m= 0 mr = 49 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 467 time to turn everything in is 0.5600000 number of dielectric boundary points 25710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14372 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) : 0.6477438 object centre at (A) : 22.54700 14.63900 3.673000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2945478E-02 1.4729764E-02 midg,1,midg; midg,igrid,midg 4.7688307E-03 7.7152057E-03 1,midg,midg; igrid,midg,midg 3.1794257E-02 -1.0089071E-02 gauss-seidel spectral radius is 0.9986104 estimated iterations to convergence 213 setup time was (sec) 0.8600000 now iterating at: 14:21:34 rms-change max change #iterations 3.656819 180.5852 at 10iterations 1.700343 74.70988 at 20iterations 0.7917243 30.04379 at 30iterations 0.3671675 14.04669 at 40iterations 0.1705581 6.538745 at 50iterations 7.9323858E-02 2.829945 at 60iterations 3.6701396E-02 1.361740 at 70iterations 1.7135432E-02 0.6443176 at 80iterations 7.9819104E-03 0.2832470 at 90iterations 3.7016042E-03 0.1335106 at 100iterations 1.7210076E-03 5.8429718E-02 at 110iterations 8.0285996E-04 2.7494431E-02 at 120iterations finished qdiffx linear iterations at : 14:21:44 total time elapsed so far: 10.59000 # loops : 120 mean,max change (kT/e) : 8.0285996E-04 2.7494431E-02 energy calculations done at 10.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 14:21:49 10.791u 0.369s 0:16.99 65.6% 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 Wed Dec 21 2011 at 14:21:50 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 = 1954 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.914847 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): -3.661000 48.75500 ymin,ymax (A): -5.272000 34.55000 zmin,zma (A): -23.80700 31.15300 x,y,z range (A): 52.41600 39.82200 54.96000 scale (grids/A): 2.914847 object centre (A): 22.54700 14.63900 3.673000 number of atom coordinates read : 1954 total number of charged atoms : 1822 net assigned charge : 4.000004 assigned positive charge : 286.9621 centred at (gu) : 100.4809 87.87138 90.01521 assigned negative charge : -282.9623 centred at (gu) : 101.0245 87.38275 89.73570 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 139012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17576 grid for indexing accessible points = 1.400000 m= 70090 mr = 99507 m= 25141 mr = 57730 m= 5448 mr = 20632 m= 622 mr = 4173 m= 15 mr = 409 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1535 time to turn everything in is 1.430000 number of dielectric boundary points 57875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14576 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) : 1.943231 object centre at (A) : 22.54700 14.63900 3.673000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8655790 1.9732744E-02 midg,1,midg; midg,igrid,midg 0.1192357 4.2934291E-02 1,midg,midg; igrid,midg,midg 0.2763586 -0.1611270 gauss-seidel spectral radius is 0.9992402 estimated iterations to convergence 286 setup time was (sec) 1.840000 now iterating at: 14:21:53 rms-change max change #iterations 8.619618 378.5909 at 10iterations 4.986731 130.9481 at 20iterations 2.863721 99.62352 at 30iterations 1.639400 37.95175 at 40iterations 0.9373353 19.37231 at 50iterations 0.5361973 11.04192 at 60iterations 0.3057517 6.195483 at 70iterations 0.1745631 3.458867 at 80iterations 9.9628314E-02 2.281013 at 90iterations 5.6593698E-02 1.068683 at 100iterations 3.2248214E-02 0.6801052 at 110iterations 1.8358402E-02 0.3648863 at 120iterations 1.0450284E-02 0.2036285 at 130iterations 5.9552663E-03 0.1231918 at 140iterations 3.3892721E-03 6.5611839E-02 at 150iterations 1.9309132E-03 3.6218643E-02 at 160iterations 1.0984448E-03 2.3120880E-02 at 170iterations 6.2423706E-04 1.2130737E-02 at 180iterations finished qdiffx linear iterations at : 14:22:06 total time elapsed so far: 15.26000 # loops : 180 mean,max change (kT/e) : 6.2423706E-04 1.2130737E-02 energy calculations done at 15.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.44000 DelPhi exited at 14:22:13 15.437u 0.629s 0:23.00 69.7% 0+0k 0+0io 0pf+0w