Tue Oct 11 07:36:04 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 Tue Oct 11 2011 at 07:36:04 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6430171 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): -1.614000 53.75000 ymin,ymax (A): -23.12500 25.88300 zmin,zma (A): 8.990000 54.60800 x,y,z range (A): 55.36400 49.00800 45.61800 scale (grids/A): 0.6430171 object centre (A): 26.06800 1.379000 31.79900 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 359.6723 centred at (gu) : 88.66637 89.48712 90.00556 assigned negative charge : -354.1728 centred at (gu) : 88.68616 89.42562 89.81970 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6678 nv = 96 ne = 84 npr = 47581 no. pairs analyzed = 47581 no. exposed pairs = 2884 no. arc points = 20595 no. surface atoms = 981 nbur = 1399 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 3715 m= 0 mr = 35 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2037 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3113936E-08 2.9783163E-08 midg,1,midg; midg,igrid,midg 1.7320118E-09 1.4173771E-08 1,midg,midg; igrid,midg,midg 1.4576071E-08 4.9441833E-09 gauss-seidel spectral radius is 0.9874498 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 07:36:04 rms-change max change #iterations 0.1485218 20.45414 at 10iterations 1.4541185E-02 2.720725 at 20iterations 1.5626750E-03 0.2143936 at 30iterations 1.7781816E-04 2.5798798E-02 at 40iterations 2.4136458E-05 3.3121109E-03 at 50iterations finished qdiffx linear iterations at : 07:36:07 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.4136458E-05 3.3121109E-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) 3.390000 DelPhi exited at 07:36:08 3.390u 0.176s 0:04.10 86.8% 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 Tue Oct 11 2011 at 07:36:08 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 1.929051 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): -1.614000 53.75000 ymin,ymax (A): -23.12500 25.88300 zmin,zma (A): 8.990000 54.60800 x,y,z range (A): 55.36400 49.00800 45.61800 scale (grids/A): 1.929051 object centre (A): 26.06800 1.379000 31.79900 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 359.6723 centred at (gu) : 85.99888 88.46102 90.01617 assigned negative charge : -354.1728 centred at (gu) : 86.05837 88.27670 89.45898 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20595 grid for indexing accessible points = 1.400000 m= 26454 mr = 49812 m= 4077 mr = 19728 m= 252 mr = 2470 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 129 time to turn everything in is 0.3600000 number of dielectric boundary points 30317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17684 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) : 0.6430171 object centre at (A) : 26.06800 1.379000 31.79900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0426549E-02 4.0349822E-02 midg,1,midg; midg,igrid,midg 5.5227982E-04 5.2548740E-03 1,midg,midg; igrid,midg,midg 2.1264207E-02 2.9452642E-02 gauss-seidel spectral radius is 0.9986502 estimated iterations to convergence 216 setup time was (sec) 0.5800000 now iterating at: 07:36:09 rms-change max change #iterations 4.126202 208.5958 at 10iterations 1.941924 77.03671 at 20iterations 0.9201597 31.12754 at 30iterations 0.4335124 14.46644 at 40iterations 0.2044284 6.839973 at 50iterations 9.6256770E-02 2.986458 at 60iterations 4.5419659E-02 1.456999 at 70iterations 2.1418547E-02 0.6765027 at 80iterations 1.0075326E-02 0.3347855 at 90iterations 4.7729746E-03 0.1577587 at 100iterations 2.2491876E-03 6.8342209E-02 at 110iterations 1.0642133E-03 3.7193298E-02 at 120iterations finished qdiffx linear iterations at : 07:36:16 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.0642133E-03 3.7193298E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 07:36:16 7.779u 0.204s 0:08.28 96.2% 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 Tue Oct 11 2011 at 07:36:16 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 2.893577 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): -1.614000 53.75000 ymin,ymax (A): -23.12500 25.88300 zmin,zma (A): 8.990000 54.60800 x,y,z range (A): 55.36400 49.00800 45.61800 scale (grids/A): 2.893577 object centre (A): 26.06800 1.379000 31.79900 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 359.6723 centred at (gu) : 83.99819 87.69125 90.02441 assigned negative charge : -354.1728 centred at (gu) : 84.08758 87.41496 89.18848 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20595 grid for indexing accessible points = 1.400000 m= 85640 mr = 120178 m= 31046 mr = 70809 m= 7167 mr = 24991 m= 1036 mr = 5183 m= 76 mr = 645 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 367 time to turn everything in is 0.9300000 number of dielectric boundary points 68407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 17951 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) : 1.929051 object centre at (A) : 26.06800 1.379000 31.79900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3009723 0.4013103 midg,1,midg; midg,igrid,midg 6.6388678E-03 -2.8140074E-02 1,midg,midg; igrid,midg,midg 0.1036684 0.2686391 gauss-seidel spectral radius is 0.9992564 estimated iterations to convergence 289 setup time was (sec) 1.170000 now iterating at: 07:36:18 rms-change max change #iterations 9.681347 393.5418 at 10iterations 5.640274 192.2899 at 20iterations 3.272208 102.9341 at 30iterations 1.890931 41.10373 at 40iterations 1.094141 22.77486 at 50iterations 0.6292813 12.01176 at 60iterations 0.3625849 6.857082 at 70iterations 0.2083730 3.874519 at 80iterations 0.1198344 2.197563 at 90iterations 6.8921901E-02 1.305492 at 100iterations 3.9523650E-02 0.7099495 at 110iterations 2.2787988E-02 0.4131203 at 120iterations 1.3058820E-02 0.2299843 at 130iterations 7.5119319E-03 0.1356306 at 140iterations 4.3281447E-03 7.5539589E-02 at 150iterations 2.4965636E-03 4.3592453E-02 at 160iterations 1.4529529E-03 2.6992798E-02 at 170iterations 8.5110631E-04 1.8428802E-02 at 180iterations finished qdiffx linear iterations at : 07:36:29 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 8.5110631E-04 1.8428802E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 07:36:30 12.509u 0.202s 0:13.30 95.4% 0+0k 0+0io 0pf+0w