Sat Oct 8 17:11:33 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+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 17:11:33 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3241 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5515361 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): 37.90500 91.88600 ymin,ymax (A): 16.66000 81.20700 zmin,zma (A): -22.02900 25.55400 x,y,z range (A): 53.98100 64.54700 47.58300 scale (grids/A): 0.5515361 object centre (A): 64.89550 48.93350 1.762500 number of atom coordinates read : 3241 total number of charged atoms : 3096 net assigned charge : -4.499984 assigned positive charge : 481.9239 centred at (gu) : 90.64006 90.38815 89.81909 assigned negative charge : -486.4250 centred at (gu) : 90.63745 90.39073 89.81068 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6439 nv = 96 ne = 84 npr = 65649 no. pairs analyzed = 65649 no. exposed pairs = 4085 no. arc points = 28253 no. surface atoms = 1375 nbur = 1866 mkacc time = 0.2200000 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= 263 mr = 3393 m= 1 mr = 13 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 0.4800000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2859 ## 370 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 8377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4151582E-10 -2.6120189E-10 midg,1,midg; midg,igrid,midg -2.9603467E-10 -4.0662620E-10 1,midg,midg; igrid,midg,midg -3.1852701E-10 -3.7755563E-10 gauss-seidel spectral radius is 0.9830670 estimated iterations to convergence 63 setup time was (sec) 0.8300000 now iterating at: 17:11:34 rms-change max change #iterations 8.1169128E-02 14.82597 at 10iterations 5.5804751E-03 0.9487267 at 20iterations 4.5586348E-04 7.4670792E-02 at 30iterations 7.2201306E-05 1.4056206E-02 at 40iterations 1.9192466E-05 4.4250488E-03 at 50iterations finished qdiffx linear iterations at : 17:11:38 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 1.9192466E-05 4.4250488E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.590000 DelPhi exited at 17:11:38 4.594u 0.400s 0:05.26 94.8% 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 Sat Oct 8 2011 at 17:11:38 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3241 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: 1.654608 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): 37.90500 91.88600 ymin,ymax (A): 16.66000 81.20700 zmin,zma (A): -22.02900 25.55400 x,y,z range (A): 53.98100 64.54700 47.58300 scale (grids/A): 1.654608 object centre (A): 64.89550 48.93350 1.762500 number of atom coordinates read : 3241 total number of charged atoms : 3096 net assigned charge : -4.499984 assigned positive charge : 481.9239 centred at (gu) : 91.91946 91.16376 89.45670 assigned negative charge : -486.4250 centred at (gu) : 91.91173 91.17173 89.43175 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 71344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 23150 mr = 49193 m= 2701 mr = 16305 m= 84 mr = 1403 m= 0 mr = 6 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 580 time to turn everything in is 0.7200000 number of dielectric boundary points 30372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 349 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 23812 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) : 0.5515361 object centre at (A) : 64.89550 48.93350 1.762500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7812406E-03 -4.3402994E-03 midg,1,midg; midg,igrid,midg 7.9468749E-03 1.9247599E-02 1,midg,midg; igrid,midg,midg -1.2316248E-02 -3.8228547E-03 gauss-seidel spectral radius is 0.9982610 estimated iterations to convergence 190 setup time was (sec) 1.040000 now iterating at: 17:11:40 rms-change max change #iterations 3.556928 162.4329 at 10iterations 1.508942 58.65762 at 20iterations 0.6428422 22.72787 at 30iterations 0.2727616 9.562999 at 40iterations 0.1164067 3.751434 at 50iterations 4.9380451E-02 1.878716 at 60iterations 2.1067414E-02 0.8246565 at 70iterations 8.9402497E-03 0.3216610 at 80iterations 3.8215159E-03 0.1224589 at 90iterations 1.6405227E-03 5.0810814E-02 at 100iterations 7.0621463E-04 2.4101257E-02 at 110iterations 3.0817249E-04 1.0406494E-02 at 120iterations finished qdiffx linear iterations at : 17:11:49 total time elapsed so far: 9.930000 # loops : 120 mean,max change (kT/e) : 3.0817249E-04 1.0406494E-02 energy calculations done at 9.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 17:11:49 10.145u 0.475s 0:10.89 97.4% 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 17:11:49 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3241 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: 2.481913 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): 37.90500 91.88600 ymin,ymax (A): 16.66000 81.20700 zmin,zma (A): -22.02900 25.55400 x,y,z range (A): 53.98100 64.54700 47.58300 scale (grids/A): 2.481913 object centre (A): 64.89550 48.93350 1.762500 number of atom coordinates read : 3241 total number of charged atoms : 3096 net assigned charge : -4.499984 assigned positive charge : 481.9239 centred at (gu) : 92.87887 91.74524 89.18481 assigned negative charge : -486.4250 centred at (gu) : 92.86757 91.75747 89.14763 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 165398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79283 mr = 120071 m= 23966 mr = 63362 m= 4428 mr = 18265 m= 396 mr = 3016 m= 4 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 1883 time to turn everything in is 1.830000 number of dielectric boundary points 68560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 24743 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) : 1.654608 object centre at (A) : 64.89550 48.93350 1.762500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9599248E-02 -3.6501724E-02 midg,1,midg; midg,igrid,midg 0.2815877 0.5523669 1,midg,midg; igrid,midg,midg -0.1905425 -1.0418099E-02 gauss-seidel spectral radius is 0.9991664 estimated iterations to convergence 274 setup time was (sec) 2.190000 now iterating at: 17:11:52 rms-change max change #iterations 9.170629 354.7602 at 10iterations 5.191963 124.5245 at 20iterations 2.925154 63.53266 at 30iterations 1.641734 32.78693 at 40iterations 0.9186448 19.94802 at 50iterations 0.5130287 10.14769 at 60iterations 0.2860777 6.407083 at 70iterations 0.1594102 3.108986 at 80iterations 8.8730536E-02 1.729492 at 90iterations 4.9418963E-02 0.9727364 at 100iterations 2.7434295E-02 0.5808489 at 110iterations 1.5263457E-02 0.2947016 at 120iterations 8.4917238E-03 0.1703987 at 130iterations 4.7381460E-03 0.1010971 at 140iterations 2.6428034E-03 5.2967072E-02 at 150iterations 1.4818306E-03 2.7844429E-02 at 160iterations 8.3792908E-04 1.5960693E-02 at 170iterations 4.7988209E-04 1.1293411E-02 at 180iterations finished qdiffx linear iterations at : 17:12:07 total time elapsed so far: 17.00000 # loops : 180 mean,max change (kT/e) : 4.7988209E-04 1.1293411E-02 energy calculations done at 17.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.21000 DelPhi exited at 17:12:07 17.211u 0.496s 0:17.97 98.4% 0+0k 0+0io 0pf+0w