Sat Oct 8 20:57:08 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 Sat Oct 8 2011 at 20:57:08 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! WARNING: HIR 116 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6161835 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): -31.27000 17.68000 ymin,ymax (A): -23.61900 23.00200 zmin,zma (A): -12.43400 45.34100 x,y,z range (A): 48.95000 46.62100 57.77500 scale (grids/A): 0.6161835 object centre (A): -6.795000 -0.3085003 16.45350 number of atom coordinates read : 2601 total number of charged atoms : 2461 net assigned charge : 3.014008 assigned positive charge : 392.9670 centred at (gu) : 88.32993 89.11999 89.65490 assigned negative charge : -389.9536 centred at (gu) : 88.25275 89.14475 89.54355 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6402 nv = 96 ne = 84 npr = 54441 no. pairs analyzed = 54441 no. exposed pairs = 3045 no. arc points = 21849 no. surface atoms = 1017 nbur = 1584 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3514 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 104 time to turn everything in is 0.2000000 number of dielectric boundary points 3161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2197 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8277600E-09 8.1453653E-09 midg,1,midg; midg,igrid,midg 4.5178812E-09 6.5458777E-10 1,midg,midg; igrid,midg,midg -3.5471854E-09 4.7145901E-09 gauss-seidel spectral radius is 0.9863579 estimated iterations to convergence 70 setup time was (sec) 0.4100000 now iterating at: 20:57:08 rms-change max change #iterations 0.1222895 19.51666 at 10iterations 1.1014692E-02 1.641270 at 20iterations 1.0051087E-03 0.1497421 at 30iterations 9.2485818E-05 1.2815952E-02 at 40iterations 8.3055775E-06 1.2519360E-03 at 50iterations finished qdiffx linear iterations at : 20:57:12 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 8.3055775E-06 1.2519360E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 20:57:12 3.739u 0.237s 0:04.24 93.3% 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 Sat Oct 8 2011 at 20:57:12 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! WARNING: HIR 116 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.848550 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): -31.27000 17.68000 ymin,ymax (A): -23.61900 23.00200 zmin,zma (A): -12.43400 45.34100 x,y,z range (A): 48.95000 46.62100 57.77500 scale (grids/A): 1.848550 object centre (A): -6.795000 -0.3085003 16.45350 number of atom coordinates read : 2601 total number of charged atoms : 2461 net assigned charge : 3.014008 assigned positive charge : 392.9670 centred at (gu) : 84.98916 87.35958 88.96432 assigned negative charge : -389.9536 centred at (gu) : 84.75819 87.43413 88.63058 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21849 grid for indexing accessible points = 1.400000 m= 23538 mr = 48611 m= 3199 mr = 17248 m= 147 mr = 1981 m= 0 mr = 46 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4750 time to turn everything in is 0.3600000 number of dielectric boundary points 29034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19293 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) : 0.6161835 object centre at (A) : -6.795000 -0.3085003 16.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0809684E-02 2.3610730E-02 midg,1,midg; midg,igrid,midg 7.4991216E-03 3.7196949E-03 1,midg,midg; igrid,midg,midg -6.4199599E-03 2.7429115E-02 gauss-seidel spectral radius is 0.9985487 estimated iterations to convergence 208 setup time was (sec) 0.5900000 now iterating at: 20:57:13 rms-change max change #iterations 3.996129 181.4383 at 10iterations 1.822198 70.15002 at 20iterations 0.8345926 34.38953 at 30iterations 0.3818503 12.55605 at 40iterations 0.1751395 5.666317 at 50iterations 8.0091782E-02 2.991879 at 60iterations 3.6538512E-02 1.142658 at 70iterations 1.6782222E-02 0.5754223 at 80iterations 7.6282914E-03 0.2608991 at 90iterations 3.4936408E-03 0.1123800 at 100iterations 1.6040893E-03 5.4834843E-02 at 110iterations 7.3257828E-04 2.2647858E-02 at 120iterations finished qdiffx linear iterations at : 20:57:20 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 7.3257828E-04 2.2647858E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 20:57:21 8.094u 0.197s 0:08.56 96.7% 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 Sat Oct 8 2011 at 20:57:21 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2601 !!! WARNING: HIR 116 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.772825 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): -31.27000 17.68000 ymin,ymax (A): -23.61900 23.00200 zmin,zma (A): -12.43400 45.34100 x,y,z range (A): 48.95000 46.62100 57.77500 scale (grids/A): 2.772825 object centre (A): -6.795000 -0.3085003 16.45350 number of atom coordinates read : 2601 total number of charged atoms : 2461 net assigned charge : 3.014008 assigned positive charge : 392.9670 centred at (gu) : 82.48374 86.03925 88.44640 assigned negative charge : -389.9536 centred at (gu) : 82.13723 86.15108 87.94590 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 162413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21849 grid for indexing accessible points = 1.400000 m= 79175 mr = 118237 m= 25611 mr = 64733 m= 5550 mr = 20390 m= 640 mr = 4211 m= 36 mr = 398 m= 0 mr = 14 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 15978 time to turn everything in is 0.9100000 number of dielectric boundary points 65442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19680 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) : 1.848550 object centre at (A) : -6.795000 -0.3085003 16.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7606708E-02 0.2680822 midg,1,midg; midg,igrid,midg 0.1177364 3.4759816E-02 1,midg,midg; igrid,midg,midg -7.3423311E-02 0.3720972 gauss-seidel spectral radius is 0.9992291 estimated iterations to convergence 284 setup time was (sec) 1.190000 now iterating at: 20:57:22 rms-change max change #iterations 9.364606 289.1058 at 10iterations 5.331160 118.7727 at 20iterations 3.020305 54.70311 at 30iterations 1.716503 33.08601 at 40iterations 0.9733556 20.00160 at 50iterations 0.5509703 10.36258 at 60iterations 0.3121892 5.741757 at 70iterations 0.1765321 3.308527 at 80iterations 0.1002479 1.804256 at 90iterations 5.6791376E-02 1.102351 at 100iterations 3.2186914E-02 0.5836866 at 110iterations 1.8258832E-02 0.3413963 at 120iterations 1.0333522E-02 0.1894684 at 130iterations 5.8624083E-03 0.1040077 at 140iterations 3.3177601E-03 6.8283081E-02 at 150iterations 1.8841944E-03 3.3315659E-02 at 160iterations 1.0712940E-03 1.9826889E-02 at 170iterations 6.0697098E-04 1.1156082E-02 at 180iterations finished qdiffx linear iterations at : 20:57:35 total time elapsed so far: 13.81000 # loops : 180 mean,max change (kT/e) : 6.0697098E-04 1.1156082E-02 energy calculations done at 13.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 20:57:35 13.951u 0.249s 0:14.46 98.1% 0+0k 0+0io 0pf+0w