Sun Oct 9 11:40:52 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 Sun Oct 9 2011 at 11:40:52 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3113 !!! WARNING: HIR 204 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5341336 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): -16.75100 49.89900 ymin,ymax (A): -24.18900 27.22900 zmin,zma (A): -19.13400 43.12700 x,y,z range (A): 66.64999 51.41800 62.26100 scale (grids/A): 0.5341336 object centre (A): 16.57400 1.520000 11.99650 number of atom coordinates read : 3113 total number of charged atoms : 3044 net assigned charge : -2.485987 assigned positive charge : 469.5612 centred at (gu) : 91.45335 90.58650 90.10963 assigned negative charge : -472.0492 centred at (gu) : 91.29382 90.65961 90.13859 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6191 nv = 96 ne = 84 npr = 56590 no. pairs analyzed = 56590 no. exposed pairs = 4669 no. arc points = 34716 no. surface atoms = 1540 nbur = 1573 mkacc time = 9.9999994E-02 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 = 1.596000 m= 257 mr = 2708 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3362 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7985 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3642576E-11 -2.4151520E-10 midg,1,midg; midg,igrid,midg 1.8840050E-10 -5.0553822E-10 1,midg,midg; igrid,midg,midg -5.7689836E-10 8.6948104E-10 gauss-seidel spectral radius is 0.9819779 estimated iterations to convergence 61 setup time was (sec) 0.4000000 now iterating at: 11:40:52 rms-change max change #iterations 6.6151924E-02 13.82646 at 10iterations 4.1362746E-03 0.7717056 at 20iterations 2.6032454E-04 4.2518616E-02 at 30iterations 1.9606472E-05 3.1757355E-03 at 40iterations 2.1597978E-06 2.8610229E-04 at 50iterations finished qdiffx linear iterations at : 11:40:55 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 2.1597978E-06 2.8610229E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 11:40:56 3.439u 0.180s 0:03.90 92.5% 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 Sun Oct 9 2011 at 11:40:56 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3113 !!! WARNING: HIR 204 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.602401 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): -16.75100 49.89900 ymin,ymax (A): -24.18900 27.22900 zmin,zma (A): -19.13400 43.12700 x,y,z range (A): 66.64999 51.41800 62.26100 scale (grids/A): 1.602401 object centre (A): 16.57400 1.520000 11.99650 number of atom coordinates read : 3113 total number of charged atoms : 3044 net assigned charge : -2.485987 assigned positive charge : 469.5612 centred at (gu) : 94.35884 91.75829 90.32797 assigned negative charge : -472.0492 centred at (gu) : 93.88097 91.97854 90.41560 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67423 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34716 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19784 mr = 41363 m= 2186 mr = 12504 m= 54 mr = 1001 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 34580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 23217 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) : 0.5341336 object centre at (A) : 16.57400 1.520000 11.99650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8856639E-03 -6.7617674E-03 midg,1,midg; midg,igrid,midg -2.4084924E-03 -6.4828424E-03 1,midg,midg; igrid,midg,midg -1.2986450E-02 2.6701482E-02 gauss-seidel spectral radius is 0.9981756 estimated iterations to convergence 186 setup time was (sec) 0.5500000 now iterating at: 11:40:56 rms-change max change #iterations 3.310680 165.6985 at 10iterations 1.374040 62.62587 at 20iterations 0.5651648 25.04533 at 30iterations 0.2338981 8.212057 at 40iterations 9.6924335E-02 3.401237 at 50iterations 4.0384673E-02 1.366624 at 60iterations 1.6694644E-02 0.5983012 at 70iterations 6.9450065E-03 0.2414131 at 80iterations 2.8791695E-03 0.1130219 at 90iterations 1.1967663E-03 4.4736862E-02 at 100iterations 4.9747113E-04 1.9556046E-02 at 110iterations 2.0775790E-04 7.3013306E-03 at 120iterations finished qdiffx linear iterations at : 11:41:04 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.0775790E-04 7.3013306E-03 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 11:41:04 7.784u 0.221s 0:08.32 96.1% 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 Sun Oct 9 2011 at 11:41:04 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3113 !!! WARNING: HIR 204 has a net charge of 0.5140 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: 2.403601 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): -16.75100 49.89900 ymin,ymax (A): -24.18900 27.22900 zmin,zma (A): -19.13400 43.12700 x,y,z range (A): 66.64999 51.41800 62.26100 scale (grids/A): 2.403601 object centre (A): 16.57400 1.520000 11.99650 number of atom coordinates read : 3113 total number of charged atoms : 3044 net assigned charge : -2.485987 assigned positive charge : 469.5612 centred at (gu) : 96.53806 92.63711 90.49143 assigned negative charge : -472.0492 centred at (gu) : 95.82149 92.96770 90.62336 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 156359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34716 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67208 mr = 102565 m= 19681 mr = 50082 m= 3344 mr = 14042 m= 197 mr = 2070 m= 5 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 77981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 24326 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) : 1.602401 object centre at (A) : 16.57400 1.520000 11.99650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2844681 -5.8322467E-02 midg,1,midg; midg,igrid,midg -7.4686661E-02 -8.7742999E-02 1,midg,midg; igrid,midg,midg -0.3680163 0.3420112 gauss-seidel spectral radius is 0.9991659 estimated iterations to convergence 273 setup time was (sec) 1.040000 now iterating at: 11:41:05 rms-change max change #iterations 8.979851 338.2564 at 10iterations 5.197993 133.4616 at 20iterations 2.994616 67.85606 at 30iterations 1.704393 44.88988 at 40iterations 0.9630697 24.70650 at 50iterations 0.5437831 12.10190 at 60iterations 0.3050287 6.989029 at 70iterations 0.1711195 3.543922 at 80iterations 9.5836036E-02 2.022104 at 90iterations 5.3485628E-02 1.106766 at 100iterations 2.9767802E-02 0.6097815 at 110iterations 1.6583432E-02 0.3338766 at 120iterations 9.2274742E-03 0.2027817 at 130iterations 5.1454273E-03 0.1081476 at 140iterations 2.8611536E-03 6.0317993E-02 at 150iterations 1.5901544E-03 3.1785965E-02 at 160iterations 8.8475697E-04 1.9481659E-02 at 170iterations 4.9176597E-04 1.1167526E-02 at 180iterations finished qdiffx linear iterations at : 11:41:17 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 4.9176597E-04 1.1167526E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 11:41:17 12.528u 0.213s 0:13.05 97.5% 0+0k 0+0io 0pf+0w