Sat Oct 15 12:58:53 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 15 2011 at 12:58:53 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7013673 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): -1.193000 46.02000 ymin,ymax (A): 36.18900 86.94700 zmin,zma (A): -24.38100 25.11500 x,y,z range (A): 47.21300 50.75800 49.49600 scale (grids/A): 0.7013673 object centre (A): 22.41350 61.56800 0.3669996 number of atom coordinates read : 2360 total number of charged atoms : 2219 net assigned charge : 3.500020 assigned positive charge : 361.7692 centred at (gu) : 90.03289 90.02593 91.53748 assigned negative charge : -358.2696 centred at (gu) : 90.16698 90.12624 91.47128 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8080 nv = 96 ne = 84 npr = 46652 no. pairs analyzed = 46652 no. exposed pairs = 3094 no. arc points = 21453 no. surface atoms = 1040 nbur = 1320 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4458 m= 4 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 4083 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1951 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8798 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4657860E-09 7.8040905E-08 midg,1,midg; midg,igrid,midg 7.3765833E-08 -2.5172268E-08 1,midg,midg; igrid,midg,midg 8.9870177E-08 -4.2422840E-08 gauss-seidel spectral radius is 0.9894399 estimated iterations to convergence 79 setup time was (sec) 0.3900000 now iterating at: 12:58:53 rms-change max change #iterations 0.2109739 26.35414 at 10iterations 2.5857689E-02 3.135633 at 20iterations 3.8311838E-03 0.5329933 at 30iterations 9.1232354E-04 0.1428108 at 40iterations 3.0579226E-04 4.5257568E-02 at 50iterations finished qdiffx linear iterations at : 12:58:56 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 3.0579226E-04 4.5257568E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 12:58:57 3.629u 0.241s 0:04.45 86.7% 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 Sat Oct 15 2011 at 12:58:57 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.104102 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): -1.193000 46.02000 ymin,ymax (A): 36.18900 86.94700 zmin,zma (A): -24.38100 25.11500 x,y,z range (A): 47.21300 50.75800 49.49600 scale (grids/A): 2.104102 object centre (A): 22.41350 61.56800 0.3669996 number of atom coordinates read : 2360 total number of charged atoms : 2219 net assigned charge : 3.500020 assigned positive charge : 361.7692 centred at (gu) : 90.09843 90.07750 94.61226 assigned negative charge : -358.2696 centred at (gu) : 90.50067 90.37838 94.41331 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21453 grid for indexing accessible points = 1.400000 m= 34440 mr = 58843 m= 6510 mr = 25791 m= 559 mr = 4200 m= 12 mr = 281 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 17604 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) : 0.7013673 object centre at (A) : 22.41350 61.56800 0.3669996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1640444E-02 2.7826848E-02 midg,1,midg; midg,igrid,midg 9.5959172E-02 1.0414253E-03 1,midg,midg; igrid,midg,midg -4.9773930E-03 -1.4715416E-02 gauss-seidel spectral radius is 0.9988534 estimated iterations to convergence 234 setup time was (sec) 0.6800000 now iterating at: 12:58:58 rms-change max change #iterations 4.960848 229.8909 at 10iterations 2.459478 78.82664 at 20iterations 1.226464 37.66056 at 30iterations 0.6130847 17.87544 at 40iterations 0.3073889 9.355563 at 50iterations 0.1539152 4.684948 at 60iterations 7.6712139E-02 2.236202 at 70iterations 3.8402539E-02 1.085760 at 80iterations 1.9412782E-02 0.5921555 at 90iterations 9.8667173E-03 0.2980118 at 100iterations 5.1077507E-03 0.1617584 at 110iterations 2.7408835E-03 8.0875397E-02 at 120iterations finished qdiffx linear iterations at : 12:59:06 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 2.7408835E-03 8.0875397E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 12:59:06 8.393u 0.234s 0:09.08 94.9% 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 Sat Oct 15 2011 at 12:59:06 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.156153 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): -1.193000 46.02000 ymin,ymax (A): 36.18900 86.94700 zmin,zma (A): -24.38100 25.11500 x,y,z range (A): 47.21300 50.75800 49.49600 scale (grids/A): 3.156153 object centre (A): 22.41350 61.56800 0.3669996 number of atom coordinates read : 2360 total number of charged atoms : 2219 net assigned charge : 3.500020 assigned positive charge : 361.7692 centred at (gu) : 90.14755 90.11606 96.91837 assigned negative charge : -358.2696 centred at (gu) : 90.75101 90.56751 96.61987 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 195738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21453 grid for indexing accessible points = 1.400000 m= 106782 mr = 142032 m= 43529 mr = 87656 m= 12085 mr = 35607 m= 2256 mr = 9129 m= 235 mr = 1619 m= 13 mr = 156 m= 0 mr = 8 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 84431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 17750 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) : 2.104102 object centre at (A) : 22.41350 61.56800 0.3669996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2766533 0.3937668 midg,1,midg; midg,igrid,midg 1.407057 -9.9576190E-02 1,midg,midg; igrid,midg,midg -0.1068479 -0.1201735 gauss-seidel spectral radius is 0.9993109 estimated iterations to convergence 301 setup time was (sec) 1.630000 now iterating at: 12:59:08 rms-change max change #iterations 11.19858 424.8683 at 10iterations 6.705072 180.3615 at 20iterations 3.999643 90.82118 at 30iterations 2.382420 43.43708 at 40iterations 1.414604 24.54857 at 50iterations 0.8400894 14.75450 at 60iterations 0.4958764 8.022525 at 70iterations 0.2931740 5.584160 at 80iterations 0.1732091 3.045712 at 90iterations 0.1022819 1.854134 at 100iterations 6.0517177E-02 1.007519 at 110iterations 3.5897944E-02 0.6164989 at 120iterations 2.1446722E-02 0.3938637 at 130iterations 1.3016716E-02 0.2697220 at 140iterations 8.1095826E-03 0.1583977 at 150iterations 5.2714008E-03 0.1116257 at 160iterations 3.6313923E-03 8.3461761E-02 at 170iterations 2.6653986E-03 5.5187225E-02 at 180iterations finished qdiffx linear iterations at : 12:59:21 total time elapsed so far: 14.37000 # loops : 180 mean,max change (kT/e) : 2.6653986E-03 5.5187225E-02 energy calculations done at 14.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.49000 DelPhi exited at 12:59:21 14.495u 0.263s 0:15.11 97.6% 0+0k 0+0io 0pf+0w