Sun Oct 9 07:48:33 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 Sun Oct 9 2011 at 07:48:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NDP 207 has a net charge of -3.0000 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: 0.7030016 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): -16.49100 30.59700 ymin,ymax (A): -20.31600 30.32400 zmin,zma (A): -4.808000 34.68900 x,y,z range (A): 47.08800 50.64000 39.49700 scale (grids/A): 0.7030016 object centre (A): 7.053000 5.004001 14.94050 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 5.000016 assigned positive charge : 333.2995 centred at (gu) : 89.94207 90.80766 90.96226 assigned negative charge : -328.2998 centred at (gu) : 89.83099 90.90455 91.11684 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7281 nv = 96 ne = 84 npr = 46494 no. pairs analyzed = 46494 no. exposed pairs = 2721 no. arc points = 19359 no. surface atoms = 919 nbur = 1301 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 527 mr = 4031 m= 7 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 3705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1804 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8305 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1814066E-08 -4.2518284E-08 midg,1,midg; midg,igrid,midg 7.2107788E-08 -8.3676692E-09 1,midg,midg; igrid,midg,midg -1.3733138E-08 8.9879038E-08 gauss-seidel spectral radius is 0.9894710 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 07:48:33 rms-change max change #iterations 0.1997570 29.07380 at 10iterations 2.4647411E-02 3.542578 at 20iterations 3.0207422E-03 0.4223938 at 30iterations 3.6118133E-04 4.3437481E-02 at 40iterations 4.4163535E-05 6.0946345E-03 at 50iterations finished qdiffx linear iterations at : 07:48:36 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 4.4163535E-05 6.0946345E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 07:48:37 3.439u 0.189s 0:03.91 92.3% 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 Sun Oct 9 2011 at 07:48:37 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NDP 207 has a net charge of -3.0000 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: 2.109005 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): -16.49100 30.59700 ymin,ymax (A): -20.31600 30.32400 zmin,zma (A): -4.808000 34.68900 x,y,z range (A): 47.08800 50.64000 39.49700 scale (grids/A): 2.109005 object centre (A): 7.053000 5.004001 14.94050 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 5.000016 assigned positive charge : 333.2995 centred at (gu) : 89.82614 92.42272 92.88654 assigned negative charge : -328.2998 centred at (gu) : 89.49281 92.71353 93.35044 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19359 grid for indexing accessible points = 1.400000 m= 30369 mr = 52693 m= 6141 mr = 22885 m= 645 mr = 4072 m= 28 mr = 332 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2340 time to turn everything in is 0.5700000 number of dielectric boundary points 34014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 16561 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) : 0.7030016 object centre at (A) : 7.053000 5.004001 14.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1716773E-02 -3.3588244E-03 midg,1,midg; midg,igrid,midg 2.6356567E-02 2.4036201E-02 1,midg,midg; igrid,midg,midg -1.4857535E-02 3.5000756E-02 gauss-seidel spectral radius is 0.9988351 estimated iterations to convergence 232 setup time was (sec) 0.8700000 now iterating at: 07:48:38 rms-change max change #iterations 4.765562 217.4673 at 10iterations 2.348590 97.64135 at 20iterations 1.161793 38.54322 at 30iterations 0.5786452 16.75887 at 40iterations 0.2864997 8.623524 at 50iterations 0.1420700 4.021042 at 60iterations 7.0492499E-02 2.110040 at 70iterations 3.4929805E-02 1.071163 at 80iterations 1.7343368E-02 0.5097329 at 90iterations 8.6038718E-03 0.2806091 at 100iterations 4.2694029E-03 0.1311462 at 110iterations 2.1169609E-03 6.7816019E-02 at 120iterations finished qdiffx linear iterations at : 07:48:45 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.1169609E-03 6.7816019E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 07:48:45 7.775u 0.223s 0:08.27 96.6% 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 07:48:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: NDP 207 has a net charge of -3.0000 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: 3.163507 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): -16.49100 30.59700 ymin,ymax (A): -20.31600 30.32400 zmin,zma (A): -4.808000 34.68900 x,y,z range (A): 47.08800 50.64000 39.49700 scale (grids/A): 3.163507 object centre (A): 7.053000 5.004001 14.94050 number of atom coordinates read : 2220 total number of charged atoms : 2083 net assigned charge : 5.000016 assigned positive charge : 333.2995 centred at (gu) : 89.73918 93.63400 94.32977 assigned negative charge : -328.2998 centred at (gu) : 89.23927 94.07021 95.02568 start vw surface at 0.1400000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 177008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19359 grid for indexing accessible points = 1.400000 m= 93678 mr = 127084 m= 39217 mr = 77365 m= 11770 mr = 32270 m= 2458 mr = 9042 m= 374 mr = 1723 m= 19 mr = 250 m= 0 mr = 5 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 8177 time to turn everything in is 1.790000 number of dielectric boundary points 76785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 16664 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) : 2.109005 object centre at (A) : 7.053000 5.004001 14.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5983273 -2.5093226E-02 midg,1,midg; midg,igrid,midg 0.1130144 0.4016181 1,midg,midg; igrid,midg,midg -9.4056033E-02 0.2339983 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.110000 now iterating at: 07:48:47 rms-change max change #iterations 10.47044 360.3683 at 10iterations 6.100772 134.6358 at 20iterations 3.551674 69.75768 at 30iterations 2.077544 36.18749 at 40iterations 1.206312 19.99663 at 50iterations 0.7030546 13.01351 at 60iterations 0.4085332 6.880799 at 70iterations 0.2379583 4.534475 at 80iterations 0.1382910 2.978722 at 90iterations 8.0525786E-02 1.331313 at 100iterations 4.6747118E-02 0.8217878 at 110iterations 2.7226068E-02 0.4659271 at 120iterations 1.5786482E-02 0.2681704 at 130iterations 9.1935582E-03 0.1659002 at 140iterations 5.3488095E-03 9.1308594E-02 at 150iterations 3.1057710E-03 4.7557831E-02 at 160iterations 1.8102777E-03 3.2587051E-02 at 170iterations 1.0513135E-03 1.9031525E-02 at 180iterations finished qdiffx linear iterations at : 07:48:58 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 1.0513135E-03 1.9031525E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 07:48:59 13.019u 0.232s 0:13.54 97.7% 0+0k 0+0io 0pf+0w