Mon Oct 10 14:19:36 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 Mon Oct 10 2011 at 14:19:36 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5912050 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): -10.31400 38.27300 ymin,ymax (A): -16.76000 39.44200 zmin,zma (A): -19.03500 41.18100 x,y,z range (A): 48.58700 56.20200 60.21600 scale (grids/A): 0.5912050 object centre (A): 13.97950 11.34100 11.07300 number of atom coordinates read : 2577 total number of charged atoms : 2420 net assigned charge : -0.9999908 assigned positive charge : 380.7070 centred at (gu) : 90.51436 89.78056 88.81464 assigned negative charge : -381.7074 centred at (gu) : 90.32687 89.88963 88.96157 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5929 nv = 96 ne = 84 npr = 52183 no. pairs analyzed = 52183 no. exposed pairs = 3421 no. arc points = 23936 no. surface atoms = 1155 nbur = 1422 mkacc time = 0.1500000 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= 267 mr = 3032 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6734057E-09 -3.3916643E-09 midg,1,midg; midg,igrid,midg 2.6638909E-09 -3.2345449E-09 1,midg,midg; igrid,midg,midg -4.9785336E-09 5.1814468E-09 gauss-seidel spectral radius is 0.9851978 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 14:19:37 rms-change max change #iterations 9.8721661E-02 17.73942 at 10iterations 8.0367578E-03 1.228254 at 20iterations 6.5832725E-04 9.9811554E-02 at 30iterations 5.3942498E-05 8.6135864E-03 at 40iterations 4.4008125E-06 7.3242188E-04 at 50iterations finished qdiffx linear iterations at : 14:19:40 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 4.4008125E-06 7.3242188E-04 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 14:19:41 4.005u 0.160s 0:04.62 90.0% 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 Mon Oct 10 2011 at 14:19:41 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 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: 1.773615 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): -10.31400 38.27300 ymin,ymax (A): -16.76000 39.44200 zmin,zma (A): -19.03500 41.18100 x,y,z range (A): 48.58700 56.20200 60.21600 scale (grids/A): 1.773615 object centre (A): 13.97950 11.34100 11.07300 number of atom coordinates read : 2577 total number of charged atoms : 2420 net assigned charge : -0.9999908 assigned positive charge : 380.7070 centred at (gu) : 91.54262 89.34133 86.44331 assigned negative charge : -381.7074 centred at (gu) : 90.98028 89.66859 86.88433 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 65056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23936 grid for indexing accessible points = 1.400000 m= 20907 mr = 43757 m= 2518 mr = 14383 m= 113 mr = 1201 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 29226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 18823 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) : 0.5912050 object centre at (A) : 13.97950 11.34100 11.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6767424E-03 1.7079939E-03 midg,1,midg; midg,igrid,midg -5.3771851E-03 -6.1909715E-03 1,midg,midg; igrid,midg,midg -2.1793751E-02 4.5124195E-03 gauss-seidel spectral radius is 0.9984294 estimated iterations to convergence 200 setup time was (sec) 1.010000 now iterating at: 14:19:42 rms-change max change #iterations 3.644600 188.8448 at 10iterations 1.598050 73.23218 at 20iterations 0.7084293 24.52735 at 30iterations 0.3145012 11.96543 at 40iterations 0.1388096 5.193634 at 50iterations 6.1490323E-02 2.406158 at 60iterations 2.7338669E-02 0.9995651 at 70iterations 1.2089442E-02 0.4375439 at 80iterations 5.3557348E-03 0.1985931 at 90iterations 2.3744339E-03 8.6859941E-02 at 100iterations 1.0503919E-03 3.3797026E-02 at 110iterations 4.6639144E-04 1.8296242E-02 at 120iterations finished qdiffx linear iterations at : 14:19:51 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 4.6639144E-04 1.8296242E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.580000 DelPhi exited at 14:19:51 9.584u 0.282s 0:10.25 96.1% 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 Mon Oct 10 2011 at 14:19:51 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2577 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.660423 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): -10.31400 38.27300 ymin,ymax (A): -16.76000 39.44200 zmin,zma (A): -19.03500 41.18100 x,y,z range (A): 48.58700 56.20200 60.21600 scale (grids/A): 2.660423 object centre (A): 13.97950 11.34100 11.07300 number of atom coordinates read : 2577 total number of charged atoms : 2420 net assigned charge : -0.9999908 assigned positive charge : 380.7070 centred at (gu) : 92.31397 89.01173 84.66486 assigned negative charge : -381.7074 centred at (gu) : 91.47034 89.50264 85.32636 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 150873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23936 grid for indexing accessible points = 1.400000 m= 70469 mr = 106960 m= 21809 mr = 55800 m= 4002 mr = 16193 m= 393 mr = 2578 m= 19 mr = 203 m= 0 mr = 7 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 65824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19350 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) : 1.773615 object centre at (A) : 13.97950 11.34100 11.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2661883E-02 6.1292563E-02 midg,1,midg; midg,igrid,midg -0.2304292 -8.4015504E-02 1,midg,midg; igrid,midg,midg -0.2623031 5.4696104E-03 gauss-seidel spectral radius is 0.9992055 estimated iterations to convergence 280 setup time was (sec) 1.930000 now iterating at: 14:19:53 rms-change max change #iterations 8.941965 328.2980 at 10iterations 5.176101 144.4536 at 20iterations 2.963781 70.66228 at 30iterations 1.688942 38.04687 at 40iterations 0.9598437 21.12626 at 50iterations 0.5447453 11.68696 at 60iterations 0.3083711 6.429806 at 70iterations 0.1742628 3.301008 at 80iterations 9.8652892E-02 1.879286 at 90iterations 5.5617712E-02 1.186073 at 100iterations 3.1448431E-02 0.6735048 at 110iterations 1.7659433E-02 0.3803177 at 120iterations 9.9800564E-03 0.1985741 at 130iterations 5.6131096E-03 0.1176021 at 140iterations 3.1631656E-03 6.5338135E-02 at 150iterations 1.7785069E-03 3.6368370E-02 at 160iterations 1.0008260E-03 1.9607544E-02 at 170iterations 5.6363415E-04 1.1617184E-02 at 180iterations finished qdiffx linear iterations at : 14:20:07 total time elapsed so far: 15.12000 # loops : 180 mean,max change (kT/e) : 5.6363415E-04 1.1617184E-02 energy calculations done at 15.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.37000 DelPhi exited at 14:20:08 15.376u 0.300s 0:16.22 96.6% 0+0k 0+0io 0pf+0w