Tue Oct 11 06:09:34 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+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 Tue Oct 11 2011 at 06:09:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7137988 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): -20.06100 24.02100 ymin,ymax (A): 0.4980000 39.10000 zmin,zma (A): 19.90200 69.77600 x,y,z range (A): 44.08200 38.60200 49.87400 scale (grids/A): 0.7137988 object centre (A): 1.980000 19.79900 44.83900 number of atom coordinates read : 2004 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 90.10859 90.99476 89.97161 assigned negative charge : -299.3222 centred at (gu) : 89.92635 90.97578 89.93855 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7065 nv = 96 ne = 84 npr = 39698 no. pairs analyzed = 39698 no. exposed pairs = 2489 no. arc points = 16990 no. surface atoms = 845 nbur = 1159 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 499 mr = 4083 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1611 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5455107E-08 9.0763585E-08 midg,1,midg; midg,igrid,midg 5.2412908E-08 1.0088851E-07 1,midg,midg; igrid,midg,midg -2.7312508E-08 1.7457130E-07 gauss-seidel spectral radius is 0.9897611 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:09:35 rms-change max change #iterations 0.2052353 27.56178 at 10iterations 2.5844309E-02 3.626333 at 20iterations 3.3340629E-03 0.4318771 at 30iterations 5.0018710E-04 6.2208176E-02 at 40iterations 1.0442962E-04 1.5235901E-02 at 50iterations finished qdiffx linear iterations at : 06:09:38 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.0442962E-04 1.5235901E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 06:09:39 4.471u 0.438s 0:05.22 93.8% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 06:09:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 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: 2.141396 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): -20.06100 24.02100 ymin,ymax (A): 0.4980000 39.10000 zmin,zma (A): 19.90200 69.77600 x,y,z range (A): 44.08200 38.60200 49.87400 scale (grids/A): 2.141396 object centre (A): 1.980000 19.79900 44.83900 number of atom coordinates read : 2004 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 90.32563 92.98447 89.91477 assigned negative charge : -299.3222 centred at (gu) : 89.77926 92.92750 89.81583 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16990 grid for indexing accessible points = 1.400000 m= 30563 mr = 52485 m= 5957 mr = 23188 m= 508 mr = 3911 m= 5 mr = 246 m= 0 mr = 2 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 31268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15108 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) : 0.7137988 object centre at (A) : 1.980000 19.79900 44.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8911985E-02 6.9604695E-02 midg,1,midg; midg,igrid,midg 3.2149234E-03 3.7775058E-02 1,midg,midg; igrid,midg,midg 1.2416684E-02 4.5811366E-02 gauss-seidel spectral radius is 0.9988439 estimated iterations to convergence 233 setup time was (sec) 1.040000 now iterating at: 06:09:40 rms-change max change #iterations 4.587789 183.1217 at 10iterations 2.283132 70.65778 at 20iterations 1.141815 39.35166 at 30iterations 0.5687452 17.80484 at 40iterations 0.2852487 9.280047 at 50iterations 0.1417865 4.318339 at 60iterations 7.0807002E-02 2.134897 at 70iterations 3.5258498E-02 1.057484 at 80iterations 1.7665077E-02 0.5222244 at 90iterations 8.8131232E-03 0.2466259 at 100iterations 4.4215028E-03 0.1451864 at 110iterations 2.2292905E-03 6.5885544E-02 at 120iterations finished qdiffx linear iterations at : 06:09:50 total time elapsed so far: 10.60000 # loops : 120 mean,max change (kT/e) : 2.2292905E-03 6.5885544E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 06:09:51 10.774u 0.463s 0:11.71 95.9% 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 Tue Oct 11 2011 at 06:09:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.212095 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): -20.06100 24.02100 ymin,ymax (A): 0.4980000 39.10000 zmin,zma (A): 19.90200 69.77600 x,y,z range (A): 44.08200 38.60200 49.87400 scale (grids/A): 3.212095 object centre (A): 1.980000 19.79900 44.83900 number of atom coordinates read : 2004 total number of charged atoms : 1901 net assigned charge : 7.500009 assigned positive charge : 306.8221 centred at (gu) : 90.48841 94.47661 89.87222 assigned negative charge : -299.3222 centred at (gu) : 89.66884 94.39137 89.72376 start vw surface at 0.1000000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 170342 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16990 grid for indexing accessible points = 1.400000 m= 94472 mr = 126236 m= 39501 mr = 78618 m= 11111 mr = 32486 m= 2041 mr = 8463 m= 234 mr = 1427 m= 12 mr = 137 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 70335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 15204 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) : 2.141396 object centre at (A) : 1.980000 19.79900 44.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6884025 0.7821935 midg,1,midg; midg,igrid,midg -1.6858830E-03 0.2859468 1,midg,midg; igrid,midg,midg 0.1809773 0.3585342 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 2.240000 now iterating at: 06:09:53 rms-change max change #iterations 10.20646 404.4342 at 10iterations 6.051930 127.8294 at 20iterations 3.590770 70.78858 at 30iterations 2.121312 41.04329 at 40iterations 1.248336 26.84591 at 50iterations 0.7348477 15.02753 at 60iterations 0.4322781 7.707366 at 70iterations 0.2542894 4.886153 at 80iterations 0.1491427 2.686535 at 90iterations 8.7584257E-02 1.779781 at 100iterations 5.1499210E-02 0.9834798 at 110iterations 3.0312095E-02 0.6061707 at 120iterations 1.7987693E-02 0.3252892 at 130iterations 1.0738033E-02 0.1910820 at 140iterations 6.5463451E-03 0.1223373 at 150iterations 4.1084103E-03 7.5630188E-02 at 160iterations 2.7067198E-03 4.9587250E-02 at 170iterations 1.8881900E-03 3.5221100E-02 at 180iterations finished qdiffx linear iterations at : 06:10:09 total time elapsed so far: 18.00000 # loops : 180 mean,max change (kT/e) : 1.8881900E-03 3.5221100E-02 energy calculations done at 18.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.16000 DelPhi exited at 06:10:10 18.168u 0.487s 0:19.07 97.7% 0+0k 0+0io 0pf+0w