Sat Oct 8 11:41:08 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 Sat Oct 8 2011 at 11:41:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.4869175 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): -53.47900 7.154000 ymin,ymax (A): -56.40500 16.70800 zmin,zma (A): -69.47000 -4.045000 x,y,z range (A): 60.63300 73.11301 65.42500 scale (grids/A): 0.4869175 object centre (A): -23.16250 -19.84850 -36.75750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : -0.4999469 assigned positive charge : 839.9419 centred at (gu) : 89.63629 90.07924 89.86201 assigned negative charge : -840.4481 centred at (gu) : 89.60316 90.11250 89.87359 start vw surface at 0.2800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 7865 nv = 96 ne = 84 npr = 113191 no. pairs analyzed = 113191 no. exposed pairs = 6916 no. arc points = 47119 no. surface atoms = 2326 nbur = 3179 mkacc time = 0.3300000 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 = 1.736000 m= 282 mr = 3998 m= 5 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 4150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4483 ## 775 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 10907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0410696E-11 -1.3924690E-11 midg,1,midg; midg,igrid,midg 3.2068993E-11 -3.8370234E-11 1,midg,midg; igrid,midg,midg -4.1393784E-11 2.9494896E-11 gauss-seidel spectral radius is 0.9784822 estimated iterations to convergence 56 setup time was (sec) 0.9400000 now iterating at: 11:41:09 rms-change max change #iterations 5.7856180E-02 8.711669 at 10iterations 4.1119168E-03 0.7731667 at 20iterations 9.3565107E-04 0.1530914 at 30iterations 3.6921937E-04 3.7322998E-02 at 40iterations 1.6309584E-04 1.5920401E-02 at 50iterations finished qdiffx linear iterations at : 11:41:13 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.6309584E-04 1.5920401E-02 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 11:41:13 4.323u 0.163s 0:05.04 88.8% 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 11:41:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2400000 grid size : 179 scale,in grids/A, set to be: 1.460752 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): -53.47900 7.154000 ymin,ymax (A): -56.40500 16.70800 zmin,zma (A): -69.47000 -4.045000 x,y,z range (A): 60.63300 73.11301 65.42500 scale (grids/A): 1.460752 object centre (A): -23.16250 -19.84850 -36.75750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : -0.4999469 assigned positive charge : 839.9419 centred at (gu) : 88.90702 90.23619 89.58409 assigned negative charge : -840.4481 centred at (gu) : 88.80933 90.33694 89.62048 start vw surface at 0.3300000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 88961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 25737 mr = 60523 m= 2084 mr = 16833 m= 37 mr = 729 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 970 time to turn everything in is 0.9000000 number of dielectric boundary points 38734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 668 ## 11 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 39344 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) : 0.4869175 object centre at (A) : -23.16250 -19.84850 -36.75750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6045657E-03 -4.5482041E-03 midg,1,midg; midg,igrid,midg 2.0926323E-02 -9.7083586E-04 1,midg,midg; igrid,midg,midg -1.3480248E-03 2.0788151E-03 gauss-seidel spectral radius is 0.9979628 estimated iterations to convergence 176 setup time was (sec) 1.250000 now iterating at: 11:41:15 rms-change max change #iterations 3.691796 152.0897 at 10iterations 1.454057 50.69278 at 20iterations 0.5756693 23.30201 at 30iterations 0.2276427 7.567039 at 40iterations 9.0619348E-02 2.777182 at 50iterations 3.6123425E-02 1.197380 at 60iterations 1.4528008E-02 0.4785423 at 70iterations 5.9849871E-03 0.2107754 at 80iterations 2.6125116E-03 8.6639404E-02 at 90iterations 1.3067533E-03 3.8181305E-02 at 100iterations 7.7422516E-04 1.9433975E-02 at 110iterations 5.2573433E-04 1.2277126E-02 at 120iterations finished qdiffx linear iterations at : 11:41:23 total time elapsed so far: 8.960000 # loops : 120 mean,max change (kT/e) : 5.2573433E-04 1.2277126E-02 energy calculations done at 8.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.190000 DelPhi exited at 11:41:23 9.193u 0.203s 0:09.67 97.1% 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 Sat Oct 8 2011 at 11:41:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5505 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1700000 grid size : 179 scale,in grids/A, set to be: 2.191128 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): -53.47900 7.154000 ymin,ymax (A): -56.40500 16.70800 zmin,zma (A): -69.47000 -4.045000 x,y,z range (A): 60.63300 73.11301 65.42500 scale (grids/A): 2.191128 object centre (A): -23.16250 -19.84850 -36.75750 number of atom coordinates read : 5505 total number of charged atoms : 5336 net assigned charge : -0.4999469 assigned positive charge : 839.9419 centred at (gu) : 88.36018 90.35381 89.37582 assigned negative charge : -840.4481 centred at (gu) : 88.21387 90.50557 89.43040 start vw surface at 0.2800000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 207541 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47119 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 92079 mr = 149315 m= 22947 mr = 71070 m= 2930 mr = 16112 m= 127 mr = 1588 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 3358 time to turn everything in is 2.000000 number of dielectric boundary points 87514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 42505 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) : 1.460752 object centre at (A) : -23.16250 -19.84850 -36.75750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1716812E-02 -4.0097348E-02 midg,1,midg; midg,igrid,midg 0.6235800 -3.4609094E-02 1,midg,midg; igrid,midg,midg 3.9399313E-03 5.4977737E-02 gauss-seidel spectral radius is 0.9991340 estimated iterations to convergence 268 setup time was (sec) 2.370000 now iterating at: 11:41:26 rms-change max change #iterations 10.47083 269.6468 at 10iterations 5.983387 147.4592 at 20iterations 3.395947 81.72356 at 30iterations 1.917085 45.13474 at 40iterations 1.081803 23.89565 at 50iterations 0.6064191 11.90725 at 60iterations 0.3387474 7.175769 at 70iterations 0.1890441 3.859848 at 80iterations 0.1050948 2.273442 at 90iterations 5.8571778E-02 1.127117 at 100iterations 3.2462623E-02 0.6983070 at 110iterations 1.8036900E-02 0.3802652 at 120iterations 1.0005643E-02 0.2000561 at 130iterations 5.5781971E-03 0.1173439 at 140iterations 3.1242729E-03 7.0244551E-02 at 150iterations 1.7750245E-03 3.9165020E-02 at 160iterations 1.0344533E-03 2.2982597E-02 at 170iterations 6.3152675E-04 1.4288902E-02 at 180iterations finished qdiffx linear iterations at : 11:41:39 total time elapsed so far: 15.65000 # loops : 180 mean,max change (kT/e) : 6.3152675E-04 1.4288902E-02 energy calculations done at 15.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.88000 DelPhi exited at 11:41:40 15.879u 0.199s 0:16.38 98.0% 0+0k 0+0io 0pf+0w