Mon Oct 10 18:47:41 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 18:47:41 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 = 2183 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: 0.6171662 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): -9.595000 48.08800 ymin,ymax (A): 63.44100 117.8920 zmin,zma (A): 47.13900 87.92900 x,y,z range (A): 57.68300 54.45100 40.79000 scale (grids/A): 0.6171662 object centre (A): 19.24650 90.66650 67.53400 number of atom coordinates read : 2183 total number of charged atoms : 2046 net assigned charge : 5.8710575E-06 assigned positive charge : 325.0822 centred at (gu) : 88.33369 90.66624 90.47567 assigned negative charge : -325.0826 centred at (gu) : 88.43418 90.73432 90.57404 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5684 nv = 96 ne = 84 npr = 43829 no. pairs analyzed = 43829 no. exposed pairs = 2846 no. arc points = 19754 no. surface atoms = 963 nbur = 1220 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3066 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2005 ## 224 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4335895E-09 -5.7000276E-09 midg,1,midg; midg,igrid,midg 2.9409388E-09 -4.1188355E-09 1,midg,midg; igrid,midg,midg 7.3655175E-09 -3.6041077E-09 gauss-seidel spectral radius is 0.9863730 estimated iterations to convergence 70 setup time was (sec) 0.4600000 now iterating at: 18:47:42 rms-change max change #iterations 0.1131132 16.39271 at 10iterations 1.0388276E-02 1.697690 at 20iterations 9.8117639E-04 0.1571541 at 30iterations 1.2050800E-04 2.0676613E-02 at 40iterations 2.3146260E-05 4.4860840E-03 at 50iterations finished qdiffx linear iterations at : 18:47:44 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 2.3146260E-05 4.4860840E-03 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 18:47:45 3.053u 0.143s 0:03.61 88.3% 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 18:47:45 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 = 2183 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: 1.851499 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): -9.595000 48.08800 ymin,ymax (A): 63.44100 117.8920 zmin,zma (A): 47.13900 87.92900 x,y,z range (A): 57.68300 54.45100 40.79000 scale (grids/A): 1.851499 object centre (A): 19.24650 90.66650 67.53400 number of atom coordinates read : 2183 total number of charged atoms : 2046 net assigned charge : 5.8710575E-06 assigned positive charge : 325.0822 centred at (gu) : 85.00064 91.99831 91.42661 assigned negative charge : -325.0826 centred at (gu) : 85.30225 92.20262 91.72191 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 22488 mr = 42021 m= 3362 mr = 16451 m= 161 mr = 1957 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 26796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 16047 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) : 0.6171662 object centre at (A) : 19.24650 90.66650 67.53400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3168980E-03 -7.6331123E-04 midg,1,midg; midg,igrid,midg 1.8029351E-02 -1.4460962E-02 1,midg,midg; igrid,midg,midg -2.9007536E-03 -1.0817816E-02 gauss-seidel spectral radius is 0.9985183 estimated iterations to convergence 206 setup time was (sec) 0.7000000 now iterating at: 18:47:46 rms-change max change #iterations 3.624525 164.6928 at 10iterations 1.633557 65.61623 at 20iterations 0.7422527 28.35145 at 30iterations 0.3355063 12.34369 at 40iterations 0.1523013 5.554685 at 50iterations 6.9092028E-02 2.504227 at 60iterations 3.1396803E-02 1.099724 at 70iterations 1.4204774E-02 0.4945025 at 80iterations 6.4602820E-03 0.2163973 at 90iterations 2.9427954E-03 0.1065369 at 100iterations 1.3465917E-03 5.3421021E-02 at 110iterations 6.1800628E-04 2.3002625E-02 at 120iterations finished qdiffx linear iterations at : 18:47:51 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 6.1800628E-04 2.3002625E-02 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 18:47:52 6.817u 0.183s 0:07.35 95.1% 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 Mon Oct 10 2011 at 18:47:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2183 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: 2.777248 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): -9.595000 48.08800 ymin,ymax (A): 63.44100 117.8920 zmin,zma (A): 47.13900 87.92900 x,y,z range (A): 57.68300 54.45100 40.79000 scale (grids/A): 2.777248 object centre (A): 19.24650 90.66650 67.53400 number of atom coordinates read : 2183 total number of charged atoms : 2046 net assigned charge : 5.8710575E-06 assigned positive charge : 325.0822 centred at (gu) : 82.50093 92.99734 92.13975 assigned negative charge : -325.0826 centred at (gu) : 82.95334 93.30390 92.58278 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 141538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19754 grid for indexing accessible points = 1.400000 m= 72239 mr = 102091 m= 26257 mr = 58698 m= 5898 mr = 20785 m= 658 mr = 4182 m= 21 mr = 332 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 60523 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 16365 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) : 1.851499 object centre at (A) : 19.24650 90.66650 67.53400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9110166E-02 2.1832319E-02 midg,1,midg; midg,igrid,midg 0.3636565 -0.1894080 1,midg,midg; igrid,midg,midg -9.3389392E-02 3.8893510E-02 gauss-seidel spectral radius is 0.9992179 estimated iterations to convergence 282 setup time was (sec) 1.340000 now iterating at: 18:47:54 rms-change max change #iterations 8.728329 322.9199 at 10iterations 5.081093 124.9379 at 20iterations 2.919471 81.62847 at 30iterations 1.673842 39.35781 at 40iterations 0.9547338 19.88601 at 50iterations 0.5446125 12.39714 at 60iterations 0.3092594 6.405161 at 70iterations 0.1753943 3.764315 at 80iterations 9.9795863E-02 2.043605 at 90iterations 5.6623150E-02 1.073256 at 100iterations 3.2058768E-02 0.7330247 at 110iterations 1.8202020E-02 0.3290749 at 120iterations 1.0307584E-02 0.2194834 at 130iterations 5.8464818E-03 0.1219149 at 140iterations 3.3204015E-03 6.8557739E-02 at 150iterations 1.8832692E-03 3.7284851E-02 at 160iterations 1.0797112E-03 2.2997379E-02 at 170iterations 6.2313920E-04 1.3244629E-02 at 180iterations finished qdiffx linear iterations at : 18:48:04 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 6.2313920E-04 1.3244629E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 18:48:05 11.809u 0.166s 0:12.40 96.4% 0+0k 0+0io 0pf+0w