Mon Oct 10 17:13:02 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+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 Mon Oct 10 2011 at 17:13:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5412884 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): -28.94000 30.10400 ymin,ymax (A): -27.42800 30.10500 zmin,zma (A): 22.33600 88.10500 x,y,z range (A): 59.04400 57.53300 65.76900 scale (grids/A): 0.5412884 object centre (A): 0.5819998 1.338500 55.22050 number of atom coordinates read : 2678 total number of charged atoms : 2542 net assigned charge : 11.00002 assigned positive charge : 393.6836 centred at (gu) : 90.47847 90.79983 91.54791 assigned negative charge : -382.6845 centred at (gu) : 90.44324 90.89571 91.36600 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5183 nv = 96 ne = 84 npr = 51948 no. pairs analyzed = 51948 no. exposed pairs = 3741 no. arc points = 26416 no. surface atoms = 1245 nbur = 1433 mkacc time = 0.1500000 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= 220 mr = 2411 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 2989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2665 ## 353 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6734 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1866688E-10 2.0742152E-09 midg,1,midg; midg,igrid,midg 8.2873269E-10 1.0685394E-10 1,midg,midg; igrid,midg,midg 3.4586434E-10 8.1405133E-10 gauss-seidel spectral radius is 0.9823923 estimated iterations to convergence 62 setup time was (sec) 0.6200000 now iterating at: 17:13:03 rms-change max change #iterations 6.3471399E-02 12.32318 at 10iterations 4.1174889E-03 0.7184868 at 20iterations 2.6105577E-04 4.5639038E-02 at 30iterations 1.7075707E-05 3.2062531E-03 at 40iterations 1.1453975E-06 2.2506714E-04 at 50iterations finished qdiffx linear iterations at : 17:13:06 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.1453975E-06 2.2506714E-04 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 17:13:07 4.140u 0.284s 0:04.70 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 Mon Oct 10 2011 at 17:13:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.623865 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): -28.94000 30.10400 ymin,ymax (A): -27.42800 30.10500 zmin,zma (A): 22.33600 88.10500 x,y,z range (A): 59.04400 57.53300 65.76900 scale (grids/A): 1.623865 object centre (A): 0.5819998 1.338500 55.22050 number of atom coordinates read : 2678 total number of charged atoms : 2542 net assigned charge : 11.00002 assigned positive charge : 393.6836 centred at (gu) : 91.43491 92.39890 94.64311 assigned negative charge : -382.6845 centred at (gu) : 91.32936 92.68698 94.09781 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 56447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16819 mr = 35830 m= 1816 mr = 10923 m= 48 mr = 707 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 27671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 329 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19422 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) : 0.5412884 object centre at (A) : 0.5819998 1.338500 55.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1887084E-02 2.0074161E-02 midg,1,midg; midg,igrid,midg 1.4413894E-02 9.1372281E-03 1,midg,midg; igrid,midg,midg 3.5163211E-03 8.8134529E-03 gauss-seidel spectral radius is 0.9981340 estimated iterations to convergence 184 setup time was (sec) 0.8100000 now iterating at: 17:13:08 rms-change max change #iterations 2.982728 160.4018 at 10iterations 1.212429 53.99491 at 20iterations 0.4967825 19.01168 at 30iterations 0.2043823 9.286530 at 40iterations 8.4184647E-02 3.174637 at 50iterations 3.4647614E-02 1.508975 at 60iterations 1.4179940E-02 0.6048946 at 70iterations 5.8210436E-03 0.2157288 at 80iterations 2.4022646E-03 9.0955734E-02 at 90iterations 9.8605501E-04 4.0119648E-02 at 100iterations 4.0668072E-04 1.7352104E-02 at 110iterations 1.6840656E-04 6.2236786E-03 at 120iterations finished qdiffx linear iterations at : 17:13:16 total time elapsed so far: 9.130000 # loops : 120 mean,max change (kT/e) : 1.6840656E-04 6.2236786E-03 energy calculations done at 9.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 17:13:17 9.310u 0.332s 0:10.07 95.7% 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 Mon Oct 10 2011 at 17:13:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2678 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.435798 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): -28.94000 30.10400 ymin,ymax (A): -27.42800 30.10500 zmin,zma (A): 22.33600 88.10500 x,y,z range (A): 59.04400 57.53300 65.76900 scale (grids/A): 2.435798 object centre (A): 0.5819998 1.338500 55.22050 number of atom coordinates read : 2678 total number of charged atoms : 2542 net assigned charge : 11.00002 assigned positive charge : 393.6836 centred at (gu) : 92.15216 93.59807 96.96441 assigned negative charge : -382.6845 centred at (gu) : 91.99409 94.03044 96.14663 start vw surface at 0.1700000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 131154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 58092 mr = 88635 m= 16209 mr = 44228 m= 2730 mr = 11489 m= 209 mr = 1508 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 62480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 20308 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) : 1.623865 object centre at (A) : 0.5819998 1.338500 55.22050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4054276 0.3610104 midg,1,midg; midg,igrid,midg 0.1781978 4.7072917E-02 1,midg,midg; igrid,midg,midg 5.6710541E-02 0.1295601 gauss-seidel spectral radius is 0.9991140 estimated iterations to convergence 265 setup time was (sec) 1.600000 now iterating at: 17:13:19 rms-change max change #iterations 7.802060 262.2567 at 10iterations 4.332860 135.6854 at 20iterations 2.398341 68.02888 at 30iterations 1.319666 31.82746 at 40iterations 0.7233637 16.58184 at 50iterations 0.3959841 8.921135 at 60iterations 0.2165155 5.352245 at 70iterations 0.1182626 2.728035 at 80iterations 6.4600892E-02 1.431042 at 90iterations 3.5166811E-02 0.7639637 at 100iterations 1.9127104E-02 0.5050507 at 110iterations 1.0418649E-02 0.2122498 at 120iterations 5.6674797E-03 0.1452217 at 130iterations 3.0893078E-03 6.6331863E-02 at 140iterations 1.6804812E-03 4.0725708E-02 at 150iterations 9.1385655E-04 2.0309448E-02 at 160iterations 4.9916271E-04 1.1602402E-02 at 170iterations 2.7096475E-04 5.9890747E-03 at 180iterations finished qdiffx linear iterations at : 17:13:33 total time elapsed so far: 15.19000 # loops : 180 mean,max change (kT/e) : 2.7096475E-04 5.9890747E-03 energy calculations done at 15.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.36000 DelPhi exited at 17:13:33 15.363u 0.329s 0:16.23 96.6% 0+0k 0+0io 0pf+0w