Sat Oct 8 14:04:14 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 14:04:15 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6407487 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): -12.16800 43.39200 ymin,ymax (A): -22.91200 22.46000 zmin,zma (A): -6.572000 47.81100 x,y,z range (A): 55.56000 45.37200 54.38300 scale (grids/A): 0.6407487 object centre (A): 15.61200 -0.2259998 20.61950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.742008 assigned positive charge : 449.8727 centred at (gu) : 88.74951 89.77659 91.30031 assigned negative charge : -448.1313 centred at (gu) : 88.64191 89.63248 91.32845 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8149 nv = 96 ne = 84 npr = 62644 no. pairs analyzed = 62644 no. exposed pairs = 3357 no. arc points = 23802 no. surface atoms = 1153 nbur = 1840 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4744 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3300000 number of dielectric boundary points 3778 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9929 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1334701E-09 -1.3111816E-09 midg,1,midg; midg,igrid,midg -1.7992440E-08 2.1293644E-08 1,midg,midg; igrid,midg,midg -1.5836457E-08 1.3369709E-08 gauss-seidel spectral radius is 0.9874108 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 14:04:15 rms-change max change #iterations 0.1555310 23.06078 at 10iterations 1.5633062E-02 2.145317 at 20iterations 1.5988461E-03 0.2103691 at 30iterations 1.6621112E-04 1.9547701E-02 at 40iterations 1.8782008E-05 2.4528503E-03 at 50iterations finished qdiffx linear iterations at : 14:04:19 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 1.8782008E-05 2.4528503E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 14:04:19 4.239u 0.245s 0:04.78 93.5% 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 14:04:19 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 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: 1.922246 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): -12.16800 43.39200 ymin,ymax (A): -22.91200 22.46000 zmin,zma (A): -6.572000 47.81100 x,y,z range (A): 55.56000 45.37200 54.38300 scale (grids/A): 1.922246 object centre (A): 15.61200 -0.2259998 20.61950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.742008 assigned positive charge : 449.8727 centred at (gu) : 86.24795 89.32966 93.90053 assigned negative charge : -448.1313 centred at (gu) : 85.92552 88.89718 93.98522 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23802 grid for indexing accessible points = 1.400000 m= 31629 mr = 64039 m= 4577 mr = 23749 m= 276 mr = 2759 m= 2 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 0.6400000 number of dielectric boundary points 34747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 22460 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) : 0.6407487 object centre at (A) : 15.61200 -0.2259998 20.61950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9804061E-04 4.0462189E-03 midg,1,midg; midg,igrid,midg -8.3783073E-03 2.9447369E-02 1,midg,midg; igrid,midg,midg -3.7259232E-02 3.1873524E-02 gauss-seidel spectral radius is 0.9986922 estimated iterations to convergence 219 setup time was (sec) 0.9800000 now iterating at: 14:04:21 rms-change max change #iterations 4.674414 175.6973 at 10iterations 2.237735 66.04737 at 20iterations 1.063620 32.80186 at 30iterations 0.5079352 13.93883 at 40iterations 0.2420884 7.434547 at 50iterations 0.1151716 3.387344 at 60iterations 5.4990567E-02 1.606901 at 70iterations 2.6192514E-02 0.8267994 at 80iterations 1.2494244E-02 0.3687887 at 90iterations 5.9579387E-03 0.1619201 at 100iterations 2.8373082E-03 7.7003479E-02 at 110iterations 1.3552919E-03 3.6828041E-02 at 120iterations finished qdiffx linear iterations at : 14:04:29 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 1.3552919E-03 3.6828041E-02 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 14:04:30 9.854u 0.282s 0:10.41 97.3% 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 14:04:30 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: HIR 111 has a net charge of 0.5140 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 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: 2.883369 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): -12.16800 43.39200 ymin,ymax (A): -22.91200 22.46000 zmin,zma (A): -6.572000 47.81100 x,y,z range (A): 55.56000 45.37200 54.38300 scale (grids/A): 2.883369 object centre (A): 15.61200 -0.2259998 20.61950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.742008 assigned positive charge : 449.8727 centred at (gu) : 84.37184 88.99438 95.85056 assigned negative charge : -448.1313 centred at (gu) : 83.88814 88.34572 95.97787 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 206084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23802 grid for indexing accessible points = 1.400000 m= 104241 mr = 154836 m= 36096 mr = 86842 m= 7980 mr = 28952 m= 1123 mr = 5755 m= 55 mr = 730 m= 0 mr = 15 time to grow re-entrant surface = 0.9899999 no. cavity mid-points inaccessible to solvent = 759 time to turn everything in is 1.680000 number of dielectric boundary points 78449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 22786 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) : 1.922246 object centre at (A) : 15.61200 -0.2259998 20.61950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1122085 0.1788640 midg,1,midg; midg,igrid,midg -7.5461082E-02 0.3088373 1,midg,midg; igrid,midg,midg -0.6009195 0.3575887 gauss-seidel spectral radius is 0.9992774 estimated iterations to convergence 294 setup time was (sec) 2.030000 now iterating at: 14:04:32 rms-change max change #iterations 10.88931 440.7479 at 10iterations 6.370113 143.0665 at 20iterations 3.708068 65.29918 at 30iterations 2.156611 41.18285 at 40iterations 1.251457 23.62510 at 50iterations 0.7253568 11.77700 at 60iterations 0.4204490 6.959358 at 70iterations 0.2436342 4.088022 at 80iterations 0.1409933 2.332878 at 90iterations 8.1594922E-02 1.317635 at 100iterations 4.7160126E-02 0.8071170 at 110iterations 2.7304228E-02 0.4784112 at 120iterations 1.5794357E-02 0.2801456 at 130iterations 9.1329515E-03 0.1564903 at 140iterations 5.2759014E-03 8.6074829E-02 at 150iterations 3.0527450E-03 5.0000906E-02 at 160iterations 1.7654670E-03 2.9752731E-02 at 170iterations 1.0231452E-03 1.6445160E-02 at 180iterations finished qdiffx linear iterations at : 14:04:46 total time elapsed so far: 15.84000 # loops : 180 mean,max change (kT/e) : 1.0231452E-03 1.6445160E-02 energy calculations done at 15.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 14:04:46 16.029u 0.288s 0:16.62 98.0% 0+0k 0+0io 0pf+0w