Sun Oct 9 10:38:37 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 10:38:37 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 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: 0.6160235 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): -1.627000 48.58800 ymin,ymax (A): -26.86100 30.92900 zmin,zma (A): -5.566000 47.48100 x,y,z range (A): 50.21500 57.79000 53.04700 scale (grids/A): 0.6160235 object centre (A): 23.48050 2.033999 20.95750 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.500014 assigned positive charge : 323.3205 centred at (gu) : 90.40186 90.96121 91.25978 assigned negative charge : -320.8213 centred at (gu) : 90.43287 90.82534 91.24702 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5657 nv = 96 ne = 84 npr = 44218 no. pairs analyzed = 44218 no. exposed pairs = 3005 no. arc points = 21386 no. surface atoms = 999 nbur = 1211 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 292 mr = 2844 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2600000 number of dielectric boundary points 3069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2126 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6914 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3712931E-10 3.0675791E-09 midg,1,midg; midg,igrid,midg -4.0344181E-09 1.0224095E-08 1,midg,midg; igrid,midg,midg 2.9455163E-09 1.9705772E-10 gauss-seidel spectral radius is 0.9863303 estimated iterations to convergence 70 setup time was (sec) 0.4600000 now iterating at: 10:38:37 rms-change max change #iterations 0.1094846 17.10038 at 10iterations 9.9208616E-03 1.765810 at 20iterations 8.6856412E-04 0.1396866 at 30iterations 7.9636178E-05 1.4715195E-02 at 40iterations 7.1715444E-06 1.2531281E-03 at 50iterations finished qdiffx linear iterations at : 10:38:40 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 7.1715444E-06 1.2531281E-03 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 10:38:40 3.026u 0.145s 0:03.47 91.0% 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 Sun Oct 9 2011 at 10:38:40 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 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: 1.848071 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): -1.627000 48.58800 ymin,ymax (A): -26.86100 30.92900 zmin,zma (A): -5.566000 47.48100 x,y,z range (A): 50.21500 57.79000 53.04700 scale (grids/A): 1.848071 object centre (A): 23.48050 2.033999 20.95750 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.500014 assigned positive charge : 323.3205 centred at (gu) : 91.20509 92.88328 93.77914 assigned negative charge : -320.8213 centred at (gu) : 91.29866 92.47609 93.74117 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21386 grid for indexing accessible points = 1.400000 m= 20256 mr = 39859 m= 3230 mr = 14114 m= 205 mr = 2048 m= 5 mr = 65 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 28556 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 16241 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) : 0.6160235 object centre at (A) : 23.48050 2.033999 20.95750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1653736E-03 3.2514453E-02 midg,1,midg; midg,igrid,midg -1.4004186E-03 2.7152114E-02 1,midg,midg; igrid,midg,midg -9.8260175E-03 -1.5957229E-02 gauss-seidel spectral radius is 0.9985218 estimated iterations to convergence 206 setup time was (sec) 0.6900000 now iterating at: 10:38:41 rms-change max change #iterations 3.669231 184.5609 at 10iterations 1.657923 68.32545 at 20iterations 0.7538633 29.21311 at 30iterations 0.3411092 12.51557 at 40iterations 0.1546469 5.374766 at 50iterations 7.0521437E-02 2.405999 at 60iterations 3.1849463E-02 1.086414 at 70iterations 1.4436172E-02 0.5295506 at 80iterations 6.5505393E-03 0.2307281 at 90iterations 2.9851724E-03 0.1166153 at 100iterations 1.3463439E-03 4.5352936E-02 at 110iterations 6.1419810E-04 2.1486282E-02 at 120iterations finished qdiffx linear iterations at : 10:38:47 total time elapsed so far: 6.550000 # loops : 120 mean,max change (kT/e) : 6.1419810E-04 2.1486282E-02 energy calculations done at 6.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.710000 DelPhi exited at 10:38:47 6.710u 0.177s 0:07.25 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 Sun Oct 9 2011 at 10:38:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 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: 2.772106 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): -1.627000 48.58800 ymin,ymax (A): -26.86100 30.92900 zmin,zma (A): -5.566000 47.48100 x,y,z range (A): 50.21500 57.79000 53.04700 scale (grids/A): 2.772106 object centre (A): 23.48050 2.033999 20.95750 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.500014 assigned positive charge : 323.3205 centred at (gu) : 91.80751 94.32491 95.66851 assigned negative charge : -320.8213 centred at (gu) : 91.94809 93.71415 95.61191 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 141190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21386 grid for indexing accessible points = 1.400000 m= 65847 mr = 97744 m= 23118 mr = 51919 m= 5754 mr = 17977 m= 834 mr = 4343 m= 50 mr = 573 m= 0 mr = 13 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 64224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 16584 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) : 1.848071 object centre at (A) : 23.48050 2.033999 20.95750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1504898 0.3975047 midg,1,midg; midg,igrid,midg -4.2163797E-02 0.2458551 1,midg,midg; igrid,midg,midg -0.1530305 -0.2153282 gauss-seidel spectral radius is 0.9992251 estimated iterations to convergence 284 setup time was (sec) 1.330000 now iterating at: 10:38:49 rms-change max change #iterations 8.648564 335.3936 at 10iterations 4.960072 125.8181 at 20iterations 2.834018 61.31005 at 30iterations 1.610048 39.22653 at 40iterations 0.9131861 19.13446 at 50iterations 0.5202140 11.37814 at 60iterations 0.2941366 5.805861 at 70iterations 0.1665108 3.477795 at 80iterations 9.4397709E-02 1.921459 at 90iterations 5.3578593E-02 1.059216 at 100iterations 3.0270630E-02 0.6166658 at 110iterations 1.7152844E-02 0.3479233 at 120iterations 9.7083971E-03 0.2058487 at 130iterations 5.4989853E-03 0.1190338 at 140iterations 3.1254394E-03 6.5685272E-02 at 150iterations 1.7681139E-03 3.6483765E-02 at 160iterations 1.0018827E-03 1.9107819E-02 at 170iterations 5.6872953E-04 1.2031555E-02 at 180iterations finished qdiffx linear iterations at : 10:38:58 total time elapsed so far: 10.46000 # loops : 180 mean,max change (kT/e) : 5.6872953E-04 1.2031555E-02 energy calculations done at 10.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 10:38:59 10.626u 0.172s 0:11.13 96.9% 0+0k 0+0io 0pf+0w