Sun Oct 9 07:48:59 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 07:48:59 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: 313 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 : 334.8994 centred at (gu) : 89.95235 90.81146 90.95550 assigned negative charge : -329.8998 centred at (gu) : 89.84467 90.90396 91.10789 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 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 0.2600000 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 0.3700000 number of grid points assigned charge 8305 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1360583E-08 -4.1649272E-08 midg,1,midg; midg,igrid,midg 7.0476950E-08 -6.1963861E-09 1,midg,midg; igrid,midg,midg -1.2342372E-08 8.8713151E-08 gauss-seidel spectral radius is 0.9894710 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 07:49:00 rms-change max change #iterations 0.2034030 29.39829 at 10iterations 2.5101278E-02 3.393826 at 20iterations 3.0708651E-03 0.4069805 at 30iterations 3.6619161E-04 4.5400620E-02 at 40iterations 4.4857010E-05 6.1383247E-03 at 50iterations finished qdiffx linear iterations at : 07:49:02 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 4.4857010E-05 6.1383247E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 07:49:03 3.343u 0.216s 0:03.89 91.2% 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 Sun Oct 9 2011 at 07:49:03 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: 313 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 : 334.8994 centred at (gu) : 89.85689 92.43410 92.86621 assigned negative charge : -329.8998 centred at (gu) : 89.53391 92.71175 93.32355 start vw surface at 0.1400000 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 = 0.2600000 no. cavity mid-points inaccessible to solvent = 2340 time to turn everything in is 0.5600000 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 0.6800000 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 6.1078064E-02 -2.5969124E-03 midg,1,midg; midg,igrid,midg 2.5205292E-02 2.3915984E-02 1,midg,midg; igrid,midg,midg -1.3646966E-02 3.4396797E-02 gauss-seidel spectral radius is 0.9988351 estimated iterations to convergence 232 setup time was (sec) 0.8400000 now iterating at: 07:49:04 rms-change max change #iterations 4.797509 217.4675 at 10iterations 2.365021 97.64134 at 20iterations 1.170097 38.23241 at 30iterations 0.5827621 17.08171 at 40iterations 0.2885149 8.736691 at 50iterations 0.1430612 4.054231 at 60iterations 7.0967332E-02 2.108890 at 70iterations 3.5177622E-02 1.099129 at 80iterations 1.7461566E-02 0.5194035 at 90iterations 8.6613996E-03 0.2774811 at 100iterations 4.2991959E-03 0.1341929 at 110iterations 2.1309291E-03 6.6371441E-02 at 120iterations finished qdiffx linear iterations at : 07:49:11 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.1309291E-03 6.6371441E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 07:49:11 7.743u 0.223s 0:08.24 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 07:49:11 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: 313 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= 5.9999999E-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 : 334.8994 centred at (gu) : 89.78529 93.65107 94.29925 assigned negative charge : -329.8998 centred at (gu) : 89.30091 94.06755 94.98537 start vw surface at 0.1300000 fill in re-entrant regions at 0.8100000 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 = 0.8600000 no. cavity mid-points inaccessible to solvent = 8177 time to turn everything in is 1.780000 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 1.920000 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 0.5917966 -1.7633226E-02 midg,1,midg; midg,igrid,midg 0.1017421 0.4002244 1,midg,midg; igrid,midg,midg -8.2355507E-02 0.2264337 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.110000 now iterating at: 07:49:13 rms-change max change #iterations 10.52888 360.3682 at 10iterations 6.135659 134.6358 at 20iterations 3.572286 69.75629 at 30iterations 2.089385 36.19521 at 40iterations 1.213301 20.29844 at 50iterations 0.7068996 13.04557 at 60iterations 0.4107384 6.880741 at 70iterations 0.2392336 4.529724 at 80iterations 0.1390171 2.972546 at 90iterations 8.0970831E-02 1.339997 at 100iterations 4.7002513E-02 0.8270965 at 110iterations 2.7373767E-02 0.4717941 at 120iterations 1.5870908E-02 0.2704430 at 130iterations 9.2434343E-03 0.1668463 at 140iterations 5.3787013E-03 9.1325760E-02 at 150iterations 3.1237355E-03 4.8164368E-02 at 160iterations 1.8206460E-03 3.2112122E-02 at 170iterations 1.0576965E-03 1.9130707E-02 at 180iterations finished qdiffx linear iterations at : 07:49:24 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.0576965E-03 1.9130707E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 07:49:25 12.960u 0.233s 0:13.51 97.6% 0+0k 0+0io 0pf+0w