Wed Feb 15 08:58:05 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:58:05 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 = 2763 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: 0.6012396 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): -1.101000 45.03200 ymin,ymax (A): -11.96700 47.24400 zmin,zma (A): -17.42700 35.86300 x,y,z range (A): 46.13300 59.21100 53.29000 scale (grids/A): 0.6012396 object centre (A): 21.96550 17.63850 9.217999 number of atom coordinates read : 2763 total number of charged atoms : 2611 net assigned charge : -3.499992 assigned positive charge : 404.6923 centred at (gu) : 90.17922 89.52660 91.22089 assigned negative charge : -408.1931 centred at (gu) : 90.24836 89.54207 91.20317 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6666 nv = 96 ne = 84 npr = 56614 no. pairs analyzed = 56614 no. exposed pairs = 3685 no. arc points = 26390 no. surface atoms = 1242 nbur = 1521 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 301 mr = 3359 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2611 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8329 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7345647E-09 -1.1140505E-09 midg,1,midg; midg,igrid,midg -1.0508623E-09 -1.9647179E-09 1,midg,midg; igrid,midg,midg 1.1159239E-09 -4.5209729E-09 gauss-seidel spectral radius is 0.9857025 estimated iterations to convergence 69 setup time was (sec) 0.6300000 now iterating at: 08:58:06 rms-change max change #iterations 0.1130695 18.25740 at 10iterations 9.5144389E-03 1.548162 at 20iterations 8.4214710E-04 0.1378860 at 30iterations 9.1030815E-05 1.3587952E-02 at 40iterations 1.6485070E-05 1.9636154E-03 at 50iterations finished qdiffx linear iterations at : 08:58:10 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 1.6485070E-05 1.9636154E-03 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.980000 DelPhi exited at 08:58:11 4.980u 0.383s 0:05.75 93.2% 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 Wed Feb 15 2012 at 08:58:11 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 = 2763 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: 1.803719 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): -1.101000 45.03200 ymin,ymax (A): -11.96700 47.24400 zmin,zma (A): -17.42700 35.86300 x,y,z range (A): 46.13300 59.21100 53.29000 scale (grids/A): 1.803719 object centre (A): 21.96550 17.63850 9.217999 number of atom coordinates read : 2763 total number of charged atoms : 2611 net assigned charge : -3.499992 assigned positive charge : 404.6923 centred at (gu) : 90.53703 88.57931 93.66175 assigned negative charge : -408.1931 centred at (gu) : 90.74466 88.62587 93.60899 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26390 grid for indexing accessible points = 1.400000 m= 23395 mr = 47954 m= 2958 mr = 16022 m= 116 mr = 1577 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 33292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20374 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) : 0.6012396 object centre at (A) : 21.96550 17.63850 9.217999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0656078E-02 5.3190794E-03 midg,1,midg; midg,igrid,midg -2.0519679E-02 7.4410206E-03 1,midg,midg; igrid,midg,midg -1.7475757E-03 -1.2501900E-02 gauss-seidel spectral radius is 0.9985072 estimated iterations to convergence 205 setup time was (sec) 0.9400000 now iterating at: 08:58:12 rms-change max change #iterations 3.905366 165.9946 at 10iterations 1.765887 62.45181 at 20iterations 0.8005683 25.65963 at 30iterations 0.3626446 12.54431 at 40iterations 0.1630647 6.246958 at 50iterations 7.4105538E-02 2.700855 at 60iterations 3.3514936E-02 1.119794 at 70iterations 1.5145358E-02 0.4722233 at 80iterations 6.8508079E-03 0.2103057 at 90iterations 3.1013007E-03 0.1002779 at 100iterations 1.4081086E-03 4.5837402E-02 at 110iterations 6.3774810E-04 2.2954941E-02 at 120iterations finished qdiffx linear iterations at : 08:58:23 total time elapsed so far: 11.83000 # loops : 120 mean,max change (kT/e) : 6.3774810E-04 2.2954941E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 08:58:24 11.998u 0.439s 0:13.01 95.4% 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 Wed Feb 15 2012 at 08:58:24 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 = 2763 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: 2.705578 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): -1.101000 45.03200 ymin,ymax (A): -11.96700 47.24400 zmin,zma (A): -17.42700 35.86300 x,y,z range (A): 46.13300 59.21100 53.29000 scale (grids/A): 2.705578 object centre (A): 21.96550 17.63850 9.217999 number of atom coordinates read : 2763 total number of charged atoms : 2611 net assigned charge : -3.499992 assigned positive charge : 404.6923 centred at (gu) : 90.80517 87.86870 95.49241 assigned negative charge : -408.1931 centred at (gu) : 91.11700 87.93874 95.41327 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 167774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26390 grid for indexing accessible points = 1.400000 m= 78086 mr = 117475 m= 24820 mr = 61212 m= 4749 mr = 18765 m= 465 mr = 3238 m= 22 mr = 231 m= 0 mr = 4 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 74991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 20880 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) : 1.803719 object centre at (A) : 21.96550 17.63850 9.217999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2436350 9.2234187E-02 midg,1,midg; midg,igrid,midg -0.2622301 0.2248856 1,midg,midg; igrid,midg,midg -6.4034738E-02 -0.1758271 gauss-seidel spectral radius is 0.9992430 estimated iterations to convergence 287 setup time was (sec) 1.840000 now iterating at: 08:58:26 rms-change max change #iterations 9.607495 269.1604 at 10iterations 5.688666 171.3697 at 20iterations 3.329008 78.25356 at 30iterations 1.940675 45.61050 at 40iterations 1.123796 25.95449 at 50iterations 0.6483284 13.36626 at 60iterations 0.3744768 7.858559 at 70iterations 0.2157978 4.454193 at 80iterations 0.1244348 2.557823 at 90iterations 7.1299829E-02 1.390196 at 100iterations 4.0915411E-02 0.8918173 at 110iterations 2.3444327E-02 0.4778142 at 120iterations 1.3448105E-02 0.2958660 at 130iterations 7.7070137E-03 0.1572971 at 140iterations 4.4059167E-03 8.1241608E-02 at 150iterations 2.5279133E-03 5.5352688E-02 at 160iterations 1.4477998E-03 2.6937485E-02 at 170iterations 8.3169242E-04 1.4722347E-02 at 180iterations finished qdiffx linear iterations at : 08:58:44 total time elapsed so far: 19.37000 # loops : 180 mean,max change (kT/e) : 8.3169242E-04 1.4722347E-02 energy calculations done at 19.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.53000 DelPhi exited at 08:58:44 19.532u 0.469s 0:20.27 98.6% 0+0k 0+0io 0pf+0w