Tue Oct 11 06:03:55 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 Tue Oct 11 2011 at 06:03:55 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7356436 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): 25.83700 72.66500 ymin,ymax (A): -18.51500 29.87800 zmin,zma (A): 4.172000 46.73600 x,y,z range (A): 46.82800 48.39300 42.56400 scale (grids/A): 0.7356436 object centre (A): 49.25100 5.681500 25.45400 number of atom coordinates read : 2220 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 89.09214 90.53060 90.12658 assigned negative charge : -313.6011 centred at (gu) : 89.23525 90.46119 90.20078 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7701 nv = 96 ne = 84 npr = 38768 no. pairs analyzed = 38768 no. exposed pairs = 2573 no. arc points = 17668 no. surface atoms = 883 nbur = 1337 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 566 mr = 4442 m= 1 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1595 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5707317E-07 2.6257995E-08 midg,1,midg; midg,igrid,midg 2.7798450E-08 1.7278690E-07 1,midg,midg; igrid,midg,midg 2.6380178E-07 -3.1275722E-08 gauss-seidel spectral radius is 0.9903599 estimated iterations to convergence 83 setup time was (sec) 0.3700000 now iterating at: 06:03:56 rms-change max change #iterations 0.2347017 35.07996 at 10iterations 3.1801172E-02 4.247939 at 20iterations 4.6567409E-03 0.6379204 at 30iterations 8.5763377E-04 0.1018438 at 40iterations 2.3168168E-04 2.7534485E-02 at 50iterations finished qdiffx linear iterations at : 06:03:59 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.3168168E-04 2.7534485E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 06:03:59 3.418u 0.183s 0:04.02 89.3% 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 Tue Oct 11 2011 at 06:03:59 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.206931 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): 25.83700 72.66500 ymin,ymax (A): -18.51500 29.87800 zmin,zma (A): 4.172000 46.73600 x,y,z range (A): 46.82800 48.39300 42.56400 scale (grids/A): 2.206931 object centre (A): 49.25100 5.681500 25.45400 number of atom coordinates read : 2220 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 87.27653 91.59200 90.37956 assigned negative charge : -313.6011 centred at (gu) : 87.70576 91.38357 90.60252 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17668 grid for indexing accessible points = 1.400000 m= 34483 mr = 57173 m= 7432 mr = 26437 m= 781 mr = 5037 m= 35 mr = 416 m= 1 mr = 7 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 0.4100000 number of dielectric boundary points 34172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15623 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) : 0.7356436 object centre at (A) : 49.25100 5.681500 25.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2797076E-02 3.1847689E-02 midg,1,midg; midg,igrid,midg 4.6083283E-02 3.6206029E-02 1,midg,midg; igrid,midg,midg 5.5335570E-02 -6.8155423E-02 gauss-seidel spectral radius is 0.9989076 estimated iterations to convergence 239 setup time was (sec) 0.6400000 now iterating at: 06:04:00 rms-change max change #iterations 4.950264 193.3518 at 10iterations 2.499878 77.59395 at 20iterations 1.275823 38.52922 at 30iterations 0.6487940 19.91717 at 40iterations 0.3282822 10.24405 at 50iterations 0.1676453 4.522911 at 60iterations 8.4834345E-02 2.520494 at 70iterations 4.3437894E-02 1.267052 at 80iterations 2.2274550E-02 0.6453972 at 90iterations 1.1414858E-02 0.3124771 at 100iterations 5.9261573E-03 0.1785431 at 110iterations 3.1394868E-03 9.4406128E-02 at 120iterations finished qdiffx linear iterations at : 06:04:07 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 3.1394868E-03 9.4406128E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 06:04:08 8.041u 0.245s 0:08.81 93.9% 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 Tue Oct 11 2011 at 06:04:08 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2220 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.310396 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): 25.83700 72.66500 ymin,ymax (A): -18.51500 29.87800 zmin,zma (A): 4.172000 46.73600 x,y,z range (A): 46.82800 48.39300 42.56400 scale (grids/A): 3.310396 object centre (A): 49.25100 5.681500 25.45400 number of atom coordinates read : 2220 total number of charged atoms : 1963 net assigned charge : 5.945010 assigned positive charge : 319.5460 centred at (gu) : 85.91460 92.38800 90.56939 assigned negative charge : -313.6011 centred at (gu) : 86.55865 92.07546 90.90374 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 185543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17668 grid for indexing accessible points = 1.400000 m= 104755 mr = 137505 m= 45836 mr = 87542 m= 14044 mr = 38027 m= 3025 mr = 11036 m= 409 mr = 2152 m= 27 mr = 257 m= 3 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 77117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 15704 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) : 2.206931 object centre at (A) : 49.25100 5.681500 25.45400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.5990404E-02 0.2385736 midg,1,midg; midg,igrid,midg 0.3616306 0.1945069 1,midg,midg; igrid,midg,midg 0.5042793 -0.7677503 gauss-seidel spectral radius is 0.9993208 estimated iterations to convergence 303 setup time was (sec) 1.530000 now iterating at: 06:04:10 rms-change max change #iterations 10.87315 310.8259 at 10iterations 6.512083 161.5179 at 20iterations 3.892866 75.69860 at 30iterations 2.317254 44.40570 at 40iterations 1.381552 25.00433 at 50iterations 0.8206056 15.24925 at 60iterations 0.4864595 8.708322 at 70iterations 0.2878911 5.095184 at 80iterations 0.1705241 2.918308 at 90iterations 0.1011847 1.796366 at 100iterations 6.0073081E-02 1.037164 at 110iterations 3.5796694E-02 0.6261559 at 120iterations 2.1557353E-02 0.3803635 at 130iterations 1.3183124E-02 0.2523804 at 140iterations 8.2492139E-03 0.1653442 at 150iterations 5.3968476E-03 0.1119843 at 160iterations 3.7288147E-03 7.3402405E-02 at 170iterations 2.7368385E-03 5.0956726E-02 at 180iterations finished qdiffx linear iterations at : 06:04:21 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 2.7368385E-03 5.0956726E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 06:04:22 13.204u 0.230s 0:14.41 93.1% 0+0k 0+0io 0pf+0w