Mon Feb 6 02:10:56 PST 2012 #!/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 Feb 6 2012 at 02:10:57 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: CYM 212 has a net charge of -0.8000 !!! WARNING: ZN 760 has a net charge of 1.6000 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: 0.5780159 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): -30.96300 30.62700 ymin,ymax (A): 8.261000 56.74400 zmin,zma (A): 37.68700 97.14400 x,y,z range (A): 61.59000 48.48300 59.45700 scale (grids/A): 0.5780159 object centre (A): -0.1680012 32.50250 67.41550 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 14.00001 assigned positive charge : 382.2677 centred at (gu) : 88.36288 90.46062 88.99625 assigned negative charge : -368.2685 centred at (gu) : 88.47687 90.48906 89.06579 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5669 nv = 96 ne = 84 npr = 50186 no. pairs analyzed = 50186 no. exposed pairs = 3376 no. arc points = 24447 no. surface atoms = 1131 nbur = 1407 mkacc time = 0.1000000 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 = 1.512000 m= 241 mr = 2780 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2400000 number of dielectric boundary points 3119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2534 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0126654E-09 1.2904284E-09 midg,1,midg; midg,igrid,midg 2.9522387E-09 2.5649427E-09 1,midg,midg; igrid,midg,midg 6.9134072E-09 6.0162125E-10 gauss-seidel spectral radius is 0.9845225 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 02:10:57 rms-change max change #iterations 8.6473003E-02 13.96280 at 10iterations 6.5833968E-03 1.026493 at 20iterations 5.1328330E-04 8.1245422E-02 at 30iterations 4.2177850E-05 7.8744888E-03 at 40iterations 3.9760780E-06 6.6280365E-04 at 50iterations finished qdiffx linear iterations at : 02:11:00 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 3.9760780E-06 6.6280365E-04 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 02:11:01 3.528u 0.183s 0:04.52 81.8% 0+0k 0+45832io 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 Feb 6 2012 at 02:11:01 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: CYM 212 has a net charge of -0.8000 !!! WARNING: ZN 760 has a net charge of 1.6000 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: 1.734048 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): -30.96300 30.62700 ymin,ymax (A): 8.261000 56.74400 zmin,zma (A): 37.68700 97.14400 x,y,z range (A): 61.59000 48.48300 59.45700 scale (grids/A): 1.734048 object centre (A): -0.1680012 32.50250 67.41550 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 14.00001 assigned positive charge : 382.2677 centred at (gu) : 85.08788 91.38120 86.98824 assigned negative charge : -368.2685 centred at (gu) : 85.43019 91.46709 87.19714 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 62261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24447 grid for indexing accessible points = 1.400000 m= 19368 mr = 40918 m= 2232 mr = 12999 m= 83 mr = 1110 m= 0 mr = 13 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 0.3900000 number of dielectric boundary points 28904 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 18608 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) : 0.5780159 object centre at (A) : -0.1680012 32.50250 67.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9190635E-02 2.0380164E-02 midg,1,midg; midg,igrid,midg 1.0565542E-02 1.7277654E-02 1,midg,midg; igrid,midg,midg 2.7362483E-02 8.2178134E-03 gauss-seidel spectral radius is 0.9983535 estimated iterations to convergence 196 setup time was (sec) 0.6000000 now iterating at: 02:11:02 rms-change max change #iterations 3.420065 185.4471 at 10iterations 1.472421 57.62809 at 20iterations 0.6400912 27.19603 at 30iterations 0.2770600 10.75661 at 40iterations 0.1203179 4.591490 at 50iterations 5.2047364E-02 1.846565 at 60iterations 2.2618340E-02 0.8233891 at 70iterations 9.7792670E-03 0.3869839 at 80iterations 4.2495239E-03 0.1631012 at 90iterations 1.8467363E-03 6.2633514E-02 at 100iterations 8.0151571E-04 2.7614653E-02 at 110iterations 3.4809107E-04 1.3313770E-02 at 120iterations finished qdiffx linear iterations at : 02:11:09 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 3.4809107E-04 1.3313770E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 02:11:10 7.921u 0.210s 0:08.82 92.1% 0+0k 0+45240io 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 Feb 6 2012 at 02:11:10 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2538 !!! WARNING: HIZ 93 has a net charge of 0.2000 !!! WARNING: CYM 212 has a net charge of -0.8000 !!! WARNING: ZN 760 has a net charge of 1.6000 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: 2.601072 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): -30.96300 30.62700 ymin,ymax (A): 8.261000 56.74400 zmin,zma (A): 37.68700 97.14400 x,y,z range (A): 61.59000 48.48300 59.45700 scale (grids/A): 2.601072 object centre (A): -0.1680012 32.50250 67.41550 number of atom coordinates read : 2538 total number of charged atoms : 2399 net assigned charge : 14.00001 assigned positive charge : 382.2677 centred at (gu) : 82.63157 92.07157 85.48213 assigned negative charge : -368.2685 centred at (gu) : 83.14524 92.20057 85.79565 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 144233 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24447 grid for indexing accessible points = 1.400000 m= 66284 mr = 100333 m= 19572 mr = 51698 m= 3536 mr = 14301 m= 330 mr = 2329 m= 11 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1972 time to turn everything in is 0.9800000 number of dielectric boundary points 65143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 19186 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) : 1.734048 object centre at (A) : -0.1680012 32.50250 67.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5213745 0.2836226 midg,1,midg; midg,igrid,midg 0.1436969 0.2845944 1,midg,midg; igrid,midg,midg 0.1439591 1.7609149E-02 gauss-seidel spectral radius is 0.9991804 estimated iterations to convergence 276 setup time was (sec) 1.200000 now iterating at: 02:11:13 rms-change max change #iterations 8.644528 299.4239 at 10iterations 4.961015 148.2196 at 20iterations 2.821577 78.21739 at 30iterations 1.592108 37.05083 at 40iterations 0.8951707 19.17492 at 50iterations 0.5044109 11.50854 at 60iterations 0.2820519 6.815126 at 70iterations 0.1579580 3.315645 at 80iterations 8.8301159E-02 1.856216 at 90iterations 4.9348693E-02 0.9802828 at 100iterations 2.7563419E-02 0.5866961 at 110iterations 1.5387975E-02 0.3140030 at 120iterations 8.5884314E-03 0.1817532 at 130iterations 4.7854106E-03 0.1060036 at 140iterations 2.6632161E-03 5.9468269E-02 at 150iterations 1.4865024E-03 2.9441833E-02 at 160iterations 8.2789041E-04 1.6839981E-02 at 170iterations 4.6137359E-04 9.7646713E-03 at 180iterations finished qdiffx linear iterations at : 02:11:24 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 4.6137359E-04 9.7646713E-03 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 02:11:25 12.628u 0.215s 0:14.96 85.7% 0+0k 0+45232io 0pf+0w