Mon Oct 10 17:06:09 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 Mon Oct 10 2011 at 17:06:10 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 = 3007 !!! WARNING: HIT 111 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5985104 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): -25.24500 34.23600 ymin,ymax (A): 3.313000 51.18700 zmin,zma (A): -3.393000 55.99800 x,y,z range (A): 59.48100 47.87400 59.39100 scale (grids/A): 0.5985104 object centre (A): 4.495501 27.25000 26.30250 number of atom coordinates read : 3007 total number of charged atoms : 2865 net assigned charge : -2.485966 assigned positive charge : 457.4579 centred at (gu) : 89.77771 90.47361 89.41203 assigned negative charge : -459.9452 centred at (gu) : 89.87352 90.60390 89.32681 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7243 nv = 96 ne = 84 npr = 59449 no. pairs analyzed = 59449 no. exposed pairs = 3963 no. arc points = 27957 no. surface atoms = 1334 nbur = 1673 mkacc time = 0.1600000 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= 364 mr = 3766 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3500000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2891 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1723426E-09 2.1922730E-09 midg,1,midg; midg,igrid,midg 3.8792694E-09 -7.1683739E-09 1,midg,midg; igrid,midg,midg 3.1051341E-09 -4.7179833E-09 gauss-seidel spectral radius is 0.9855949 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 17:06:11 rms-change max change #iterations 0.1189830 19.51804 at 10iterations 9.8968828E-03 1.499807 at 20iterations 8.2312006E-04 0.1256969 at 30iterations 7.0765993E-05 1.1425018E-02 at 40iterations 6.1580758E-06 1.1291504E-03 at 50iterations finished qdiffx linear iterations at : 17:06:14 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 6.1580758E-06 1.1291504E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 17:06:15 4.499u 0.368s 0:05.58 86.9% 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 17:06:15 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 = 3007 !!! WARNING: HIT 111 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.795531 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): -25.24500 34.23600 ymin,ymax (A): 3.313000 51.18700 zmin,zma (A): -3.393000 55.99800 x,y,z range (A): 59.48100 47.87400 59.39100 scale (grids/A): 1.795531 object centre (A): 4.495501 27.25000 26.30250 number of atom coordinates read : 3007 total number of charged atoms : 2865 net assigned charge : -2.485966 assigned positive charge : 457.4579 centred at (gu) : 89.33239 91.41991 88.23524 assigned negative charge : -459.9452 centred at (gu) : 89.62016 91.81141 87.98009 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27957 grid for indexing accessible points = 1.400000 m= 26002 mr = 53678 m= 3068 mr = 18105 m= 115 mr = 1465 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1106 time to turn everything in is 0.6400000 number of dielectric boundary points 35314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 22385 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) : 0.5985104 object centre at (A) : 4.495501 27.25000 26.30250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8150835E-03 1.6772026E-02 midg,1,midg; midg,igrid,midg 6.7915116E-03 -1.9986963E-02 1,midg,midg; igrid,midg,midg 2.5669686E-02 -2.8502008E-02 gauss-seidel spectral radius is 0.9985188 estimated iterations to convergence 206 setup time was (sec) 0.9400000 now iterating at: 17:06:17 rms-change max change #iterations 4.173584 191.1092 at 10iterations 1.886784 69.91408 at 20iterations 0.8490964 26.64711 at 30iterations 0.3859200 13.56900 at 40iterations 0.1744654 5.531265 at 50iterations 7.9105258E-02 3.016094 at 60iterations 3.5819434E-02 1.157896 at 70iterations 1.6259732E-02 0.5021095 at 80iterations 7.3838918E-03 0.2522583 at 90iterations 3.3487778E-03 0.1093473 at 100iterations 1.5162034E-03 4.7092438E-02 at 110iterations 6.8770541E-04 2.0870209E-02 at 120iterations finished qdiffx linear iterations at : 17:06:26 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 6.8770541E-04 2.0870209E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.58000 DelPhi exited at 17:06:27 10.585u 0.417s 0:11.42 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 Mon Oct 10 2011 at 17:06:27 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 = 3007 !!! WARNING: HIT 111 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.693297 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): -25.24500 34.23600 ymin,ymax (A): 3.313000 51.18700 zmin,zma (A): -3.393000 55.99800 x,y,z range (A): 59.48100 47.87400 59.39100 scale (grids/A): 2.693297 object centre (A): 4.495501 27.25000 26.30250 number of atom coordinates read : 3007 total number of charged atoms : 2865 net assigned charge : -2.485966 assigned positive charge : 457.4579 centred at (gu) : 88.99821 92.12960 87.35268 assigned negative charge : -459.9452 centred at (gu) : 89.43012 92.71711 86.97011 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 183893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27957 grid for indexing accessible points = 1.400000 m= 87249 mr = 131002 m= 27442 mr = 69233 m= 5020 mr = 20845 m= 499 mr = 3200 m= 17 mr = 242 m= 0 mr = 7 time to grow re-entrant surface = 0.9800001 no. cavity mid-points inaccessible to solvent = 3734 time to turn everything in is 1.610000 number of dielectric boundary points 79591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 22917 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) : 1.795531 object centre at (A) : 4.495501 27.25000 26.30250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2164583 0.2172503 midg,1,midg; midg,igrid,midg 9.6142620E-02 -0.1850292 1,midg,midg; igrid,midg,midg 0.4491645 -0.3185580 gauss-seidel spectral radius is 0.9992459 estimated iterations to convergence 287 setup time was (sec) 1.970000 now iterating at: 17:06:29 rms-change max change #iterations 10.17424 274.9698 at 10iterations 5.961400 145.2049 at 20iterations 3.453381 84.13097 at 30iterations 1.990932 41.34446 at 40iterations 1.145563 23.13454 at 50iterations 0.6582245 12.56713 at 60iterations 0.3779625 7.035065 at 70iterations 0.2162291 4.452865 at 80iterations 0.1237554 2.182236 at 90iterations 7.0711203E-02 1.410091 at 100iterations 4.0491767E-02 0.7424059 at 110iterations 2.3105389E-02 0.4190850 at 120iterations 1.3230367E-02 0.2278309 at 130iterations 7.5353268E-03 0.1549988 at 140iterations 4.3090540E-03 7.4462891E-02 at 150iterations 2.4634195E-03 4.3258190E-02 at 160iterations 1.4029020E-03 2.7327061E-02 at 170iterations 8.0396945E-04 1.5231609E-02 at 180iterations finished qdiffx linear iterations at : 17:06:45 total time elapsed so far: 18.08000 # loops : 180 mean,max change (kT/e) : 8.0396945E-04 1.5231609E-02 energy calculations done at 18.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 17:06:46 18.246u 0.470s 0:19.03 98.3% 0+0k 0+0io 0pf+0w