Tue Oct 11 07:14:39 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 Tue Oct 11 2011 at 07:14:39 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5917356 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): 0.6920000 48.95800 ymin,ymax (A): -8.689000 49.23000 zmin,zma (A): 0.9160000 61.07800 x,y,z range (A): 48.26600 57.91900 60.16200 scale (grids/A): 0.5917356 object centre (A): 24.82500 20.27050 30.99700 number of atom coordinates read : 3242 total number of charged atoms : 3090 net assigned charge : -0.5999916 assigned positive charge : 486.5879 centred at (gu) : 89.68671 89.64154 90.87573 assigned negative charge : -487.1890 centred at (gu) : 89.59303 89.55303 90.80483 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7483 nv = 96 ne = 84 npr = 66370 no. pairs analyzed = 66370 no. exposed pairs = 3870 no. arc points = 26145 no. surface atoms = 1322 nbur = 1920 mkacc time = 0.2200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 382 mr = 4320 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.4700000 number of dielectric boundary points 3512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2643 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 9480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2170563E-09 2.8183023E-09 midg,1,midg; midg,igrid,midg -3.6439090E-09 2.6679416E-09 1,midg,midg; igrid,midg,midg -3.8067487E-09 2.8626801E-09 gauss-seidel spectral radius is 0.9852724 estimated iterations to convergence 68 setup time was (sec) 0.7800000 now iterating at: 07:14:41 rms-change max change #iterations 0.1147038 18.24812 at 10iterations 1.0127822E-02 1.518343 at 20iterations 1.3519502E-03 0.2104645 at 30iterations 4.1402914E-04 6.5081596E-02 at 40iterations 1.5402984E-04 2.4251938E-02 at 50iterations finished qdiffx linear iterations at : 07:14:44 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 1.5402984E-04 2.4251938E-02 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 07:14:45 4.552u 0.448s 0:05.50 90.7% 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 Tue Oct 11 2011 at 07:14:45 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.775207 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): 0.6920000 48.95800 ymin,ymax (A): -8.689000 49.23000 zmin,zma (A): 0.9160000 61.07800 x,y,z range (A): 48.26600 57.91900 60.16200 scale (grids/A): 1.775207 object centre (A): 24.82500 20.27050 30.99700 number of atom coordinates read : 3242 total number of charged atoms : 3090 net assigned charge : -0.5999916 assigned positive charge : 486.5879 centred at (gu) : 89.05939 88.92352 92.62627 assigned negative charge : -487.1890 centred at (gu) : 88.77876 88.65915 92.41386 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 82717 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 30271 mr = 59197 m= 4103 mr = 22915 m= 130 mr = 2518 m= 0 mr = 43 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 796 time to turn everything in is 0.8400000 number of dielectric boundary points 32548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 24060 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) : 0.5917356 object centre at (A) : 24.82500 20.27050 30.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3385132E-02 5.4649310E-03 midg,1,midg; midg,igrid,midg -1.5497765E-02 6.3125165E-03 1,midg,midg; igrid,midg,midg -1.1199390E-02 2.7026758E-03 gauss-seidel spectral radius is 0.9984982 estimated iterations to convergence 205 setup time was (sec) 1.160000 now iterating at: 07:14:47 rms-change max change #iterations 4.229527 162.6202 at 10iterations 1.908084 64.93076 at 20iterations 0.8642011 24.95654 at 30iterations 0.3918330 12.59663 at 40iterations 0.1774971 5.686999 at 50iterations 8.0621287E-02 2.495563 at 60iterations 3.6641423E-02 1.134716 at 70iterations 1.6727062E-02 0.5356216 at 80iterations 7.7208290E-03 0.2288675 at 90iterations 3.6765567E-03 0.1263298 at 100iterations 1.8431742E-03 6.5843582E-02 at 110iterations 9.9858420E-04 3.7417889E-02 at 120iterations finished qdiffx linear iterations at : 07:14:56 total time elapsed so far: 10.22000 # loops : 120 mean,max change (kT/e) : 9.9858420E-04 3.7417889E-02 energy calculations done at 10.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.44000 DelPhi exited at 07:14:56 10.449u 0.471s 0:11.46 95.2% 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 07:14:57 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3242 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.662810 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): 0.6920000 48.95800 ymin,ymax (A): -8.689000 49.23000 zmin,zma (A): 0.9160000 61.07800 x,y,z range (A): 48.26600 57.91900 60.16200 scale (grids/A): 2.662810 object centre (A): 24.82500 20.27050 30.99700 number of atom coordinates read : 3242 total number of charged atoms : 3090 net assigned charge : -0.5999916 assigned positive charge : 486.5879 centred at (gu) : 88.58891 88.38522 93.93922 assigned negative charge : -487.1890 centred at (gu) : 88.16808 87.98856 93.62070 start vw surface at 0.1800000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 191494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26145 grid for indexing accessible points = 1.400000 m= 99727 mr = 143187 m= 34302 mr = 82913 m= 6935 mr = 28023 m= 702 mr = 5205 m= 17 mr = 428 m= 0 mr = 0 time to grow re-entrant surface = 1.330000 no. cavity mid-points inaccessible to solvent = 2693 time to turn everything in is 2.160000 number of dielectric boundary points 73421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 24711 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) : 1.775207 object centre at (A) : 24.82500 20.27050 30.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3309679 -6.3246801E-02 midg,1,midg; midg,igrid,midg -0.3121370 0.1057987 1,midg,midg; igrid,midg,midg -0.1363730 3.9397174E-04 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 2.530000 now iterating at: 07:15:00 rms-change max change #iterations 10.24776 333.3987 at 10iterations 5.958534 145.9990 at 20iterations 3.439066 74.19991 at 30iterations 1.970628 43.16617 at 40iterations 1.132601 22.76152 at 50iterations 0.6481368 12.06410 at 60iterations 0.3709873 6.504097 at 70iterations 0.2112647 3.915833 at 80iterations 0.1206161 2.379557 at 90iterations 6.8743251E-02 1.137184 at 100iterations 3.9233059E-02 0.6836643 at 110iterations 2.2400469E-02 0.4141994 at 120iterations 1.2832038E-02 0.2486725 at 130iterations 7.4065360E-03 0.1323471 at 140iterations 4.3252576E-03 7.8401566E-02 at 150iterations 2.5949152E-03 4.9291611E-02 at 160iterations 1.6212250E-03 3.2740116E-02 at 170iterations 1.0699967E-03 2.0982742E-02 at 180iterations finished qdiffx linear iterations at : 07:15:15 total time elapsed so far: 17.68000 # loops : 180 mean,max change (kT/e) : 1.0699967E-03 2.0982742E-02 energy calculations done at 17.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.90000 DelPhi exited at 07:15:16 17.904u 0.495s 0:19.01 96.7% 0+0k 0+0io 0pf+0w