Sat Oct 8 11:38:36 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 11:38:36 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIQ 440 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5688991 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): -27.87300 34.70400 ymin,ymax (A): 38.12300 98.17600 zmin,zma (A): 30.38900 89.69900 x,y,z range (A): 62.57700 60.05300 59.31000 scale (grids/A): 0.5688991 object centre (A): 3.415499 68.14951 60.04400 number of atom coordinates read : 4461 total number of charged atoms : 4313 net assigned charge : -2.485956 assigned positive charge : 673.2993 centred at (gu) : 90.89710 88.31116 88.48830 assigned negative charge : -675.7882 centred at (gu) : 90.78521 88.39942 88.58112 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9064 nv = 96 ne = 84 npr = 95093 no. pairs analyzed = 95093 no. exposed pairs = 4775 no. arc points = 32618 no. surface atoms = 1635 nbur = 2826 mkacc time = 0.2500000 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= 399 mr = 5391 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.4900000 number of dielectric boundary points 4040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3420 ## 398 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 12082 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3799354E-09 -1.8166308E-09 midg,1,midg; midg,igrid,midg 2.3335658E-09 -1.6711442E-09 1,midg,midg; igrid,midg,midg -2.4620845E-09 2.5717499E-09 gauss-seidel spectral radius is 0.9841555 estimated iterations to convergence 65 setup time was (sec) 0.8300000 now iterating at: 11:38:37 rms-change max change #iterations 0.1128947 13.85094 at 10iterations 8.8380035E-03 1.007277 at 20iterations 9.2801562E-04 0.1181111 at 30iterations 2.2716426E-04 3.2315254E-02 at 40iterations 7.9480560E-05 1.1545956E-02 at 50iterations finished qdiffx linear iterations at : 11:38:42 total time elapsed so far: 5.260000 # loops : 50 mean,max change (kT/e) : 7.9480560E-05 1.1545956E-02 energy calculations done at 5.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.440000 DelPhi exited at 11:38:42 5.447u 0.474s 0:06.24 94.7% 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 8 2011 at 11:38:42 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIQ 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.706697 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): -27.87300 34.70400 ymin,ymax (A): 38.12300 98.17600 zmin,zma (A): 30.38900 89.69900 x,y,z range (A): 62.57700 60.05300 59.31000 scale (grids/A): 1.706697 object centre (A): 3.415499 68.14951 60.04400 number of atom coordinates read : 4461 total number of charged atoms : 4313 net assigned charge : -2.485956 assigned positive charge : 673.2993 centred at (gu) : 92.68981 84.93271 85.46355 assigned negative charge : -675.7882 centred at (gu) : 92.35547 85.19773 85.74280 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 101282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32618 grid for indexing accessible points = 1.400000 m= 34724 mr = 74417 m= 4287 mr = 25933 m= 146 mr = 2575 m= 0 mr = 25 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 5030 time to turn everything in is 0.8400000 number of dielectric boundary points 37489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 336 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 33373 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) : 0.5688991 object centre at (A) : 3.415499 68.14951 60.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8060754E-03 -2.4291625E-02 midg,1,midg; midg,igrid,midg 3.6436472E-02 3.6809277E-03 1,midg,midg; igrid,midg,midg -1.9954385E-02 3.4057084E-02 gauss-seidel spectral radius is 0.9984587 estimated iterations to convergence 202 setup time was (sec) 1.190000 now iterating at: 11:38:44 rms-change max change #iterations 4.645074 191.4367 at 10iterations 2.076256 62.40758 at 20iterations 0.9325541 29.49055 at 30iterations 0.4160027 12.92225 at 40iterations 0.1865903 4.814867 at 50iterations 8.3310798E-02 2.440350 at 60iterations 3.7449274E-02 1.036240 at 70iterations 1.6826810E-02 0.4926567 at 80iterations 7.5817155E-03 0.2064056 at 90iterations 3.4493073E-03 9.8106384E-02 at 100iterations 1.5930701E-03 4.2587280E-02 at 110iterations 7.5952889E-04 2.2575378E-02 at 120iterations finished qdiffx linear iterations at : 11:38:56 total time elapsed so far: 12.72000 # loops : 120 mean,max change (kT/e) : 7.5952889E-04 2.2575378E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 11:38:56 12.891u 0.547s 0:13.70 98.0% 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 11:38:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4461 !!! WARNING: HIQ 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.560046 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): -27.87300 34.70400 ymin,ymax (A): 38.12300 98.17600 zmin,zma (A): 30.38900 89.69900 x,y,z range (A): 62.57700 60.05300 59.31000 scale (grids/A): 2.560046 object centre (A): 3.415499 68.14951 60.04400 number of atom coordinates read : 4461 total number of charged atoms : 4313 net assigned charge : -2.485956 assigned positive charge : 673.2993 centred at (gu) : 94.03449 82.39891 83.19501 assigned negative charge : -675.7882 centred at (gu) : 93.53308 82.79644 83.61421 start vw surface at 0.1700000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 235936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32618 grid for indexing accessible points = 1.400000 m= 117736 mr = 180341 m= 37329 mr = 98166 m= 7300 mr = 30131 m= 665 mr = 5444 m= 15 mr = 378 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.310000 no. cavity mid-points inaccessible to solvent = 16803 time to turn everything in is 2.150000 number of dielectric boundary points 84521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 34481 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) : 1.706697 object centre at (A) : 3.415499 68.14951 60.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.3484881E-02 -0.2907542 midg,1,midg; midg,igrid,midg 0.4960504 -1.7599588E-02 1,midg,midg; igrid,midg,midg -0.2821562 0.2905067 gauss-seidel spectral radius is 0.9992355 estimated iterations to convergence 285 setup time was (sec) 2.570000 now iterating at: 11:38:59 rms-change max change #iterations 11.41321 292.5950 at 10iterations 6.597924 137.5363 at 20iterations 3.795616 71.76219 at 30iterations 2.180885 39.07830 at 40iterations 1.248304 21.60850 at 50iterations 0.7155600 12.70034 at 60iterations 0.4079071 7.608825 at 70iterations 0.2332625 3.604233 at 80iterations 0.1333229 2.318733 at 90iterations 7.5974084E-02 1.177914 at 100iterations 4.3424081E-02 0.7043152 at 110iterations 2.4778740E-02 0.4338622 at 120iterations 1.4126340E-02 0.2217299 at 130iterations 8.0805477E-03 0.1451130 at 140iterations 4.6217474E-03 7.2191238E-02 at 150iterations 2.6473722E-03 4.3221474E-02 at 160iterations 1.5292445E-03 2.3729533E-02 at 170iterations 8.8978262E-04 1.4169693E-02 at 180iterations finished qdiffx linear iterations at : 11:39:19 total time elapsed so far: 22.33000 # loops : 180 mean,max change (kT/e) : 8.8978262E-04 1.4169693E-02 energy calculations done at 22.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.50000 DelPhi exited at 11:39:19 22.506u 0.550s 0:23.31 98.8% 0+0k 0+0io 0pf+0w