Sat Oct 15 15:26:11 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 15:26:11 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6461566 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): -11.34900 36.66800 ymin,ymax (A): -25.77400 22.69700 zmin,zma (A): -9.860001 45.23500 x,y,z range (A): 48.01700 48.47100 55.09500 scale (grids/A): 0.6461566 object centre (A): 12.65950 -1.538500 17.68750 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.154013 assigned positive charge : 413.8958 centred at (gu) : 90.19856 90.28899 91.80201 assigned negative charge : -410.7423 centred at (gu) : 89.93249 90.11521 91.74720 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7513 nv = 96 ne = 84 npr = 56560 no. pairs analyzed = 56560 no. exposed pairs = 3308 no. arc points = 22947 no. surface atoms = 1118 nbur = 1615 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 4260 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2100000 number of dielectric boundary points 3617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2304 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9143 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8284901E-09 1.9297499E-08 midg,1,midg; midg,igrid,midg -1.9266945E-08 3.1910776E-08 1,midg,midg; igrid,midg,midg -3.3129371E-08 4.4649237E-08 gauss-seidel spectral radius is 0.9875951 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 15:26:12 rms-change max change #iterations 0.1594986 21.18204 at 10iterations 1.6380828E-02 2.115278 at 20iterations 1.7676230E-03 0.2204361 at 30iterations 2.2670758E-04 3.7172318E-02 at 40iterations 4.6321838E-05 6.6795349E-03 at 50iterations finished qdiffx linear iterations at : 15:26:18 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 4.6321838E-05 6.6795349E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 15:26:19 3.523u 0.180s 0:07.94 46.5% 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 15:26:19 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.938470 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): -11.34900 36.66800 ymin,ymax (A): -25.77400 22.69700 zmin,zma (A): -9.860001 45.23500 x,y,z range (A): 48.01700 48.47100 55.09500 scale (grids/A): 1.938470 object centre (A): 12.65950 -1.538500 17.68750 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.154013 assigned positive charge : 413.8958 centred at (gu) : 90.59498 90.86641 95.40546 assigned negative charge : -410.7423 centred at (gu) : 89.79700 90.34534 95.24130 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 81278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22947 grid for indexing accessible points = 1.400000 m= 29690 mr = 57438 m= 4352 mr = 22030 m= 237 mr = 2711 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 863 time to turn everything in is 0.4000000 number of dielectric boundary points 33315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 20356 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) : 0.6461566 object centre at (A) : 12.65950 -1.538500 17.68750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8558299E-02 6.9091781E-03 midg,1,midg; midg,igrid,midg -1.3332277E-02 2.9099341E-02 1,midg,midg; igrid,midg,midg -1.6124437E-02 5.9162058E-02 gauss-seidel spectral radius is 0.9986904 estimated iterations to convergence 219 setup time was (sec) 0.6200000 now iterating at: 15:26:20 rms-change max change #iterations 4.554316 200.9890 at 10iterations 2.170918 75.74668 at 20iterations 1.033978 31.84487 at 30iterations 0.4935457 17.51141 at 40iterations 0.2347419 7.324383 at 50iterations 0.1120936 3.377512 at 60iterations 5.3310703E-02 1.946449 at 70iterations 2.5473591E-02 0.8112600 at 80iterations 1.2155323E-02 0.4199600 at 90iterations 5.7836887E-03 0.1812601 at 100iterations 2.7606892E-03 8.8405609E-02 at 110iterations 1.3236492E-03 4.3111801E-02 at 120iterations finished qdiffx linear iterations at : 15:26:35 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 1.3236492E-03 4.3111801E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 15:26:36 8.178u 0.217s 0:16.30 51.4% 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 15:26:36 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 71 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.907705 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): -11.34900 36.66800 ymin,ymax (A): -25.77400 22.69700 zmin,zma (A): -9.860001 45.23500 x,y,z range (A): 48.01700 48.47100 55.09500 scale (grids/A): 2.907705 object centre (A): 12.65950 -1.538500 17.68750 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.154013 assigned positive charge : 413.8958 centred at (gu) : 90.89236 91.29961 98.10800 assigned negative charge : -410.7423 centred at (gu) : 89.69544 90.51788 97.86186 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 187793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22947 grid for indexing accessible points = 1.400000 m= 96303 mr = 138513 m= 34388 mr = 79443 m= 7827 mr = 27758 m= 1009 mr = 5792 m= 58 mr = 659 m= 0 mr = 19 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 3067 time to turn everything in is 1.120000 number of dielectric boundary points 75194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20644 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) : 1.938470 object centre at (A) : 12.65950 -1.538500 17.68750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4046416 0.2991709 midg,1,midg; midg,igrid,midg -0.1605422 0.3255886 1,midg,midg; igrid,midg,midg -0.1275103 0.4948032 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.430000 now iterating at: 15:26:37 rms-change max change #iterations 10.56946 441.8905 at 10iterations 6.184316 177.9961 at 20iterations 3.616096 80.48821 at 30iterations 2.110325 39.83146 at 40iterations 1.225464 23.44598 at 50iterations 0.7120955 13.59343 at 60iterations 0.4132564 8.000740 at 70iterations 0.2393385 4.069107 at 80iterations 0.1386435 2.435036 at 90iterations 8.0287784E-02 1.410772 at 100iterations 4.6485670E-02 0.7943950 at 110iterations 2.6913548E-02 0.4749646 at 120iterations 1.5609392E-02 0.2625828 at 130iterations 9.0371314E-03 0.1642761 at 140iterations 5.2566524E-03 9.4856262E-02 at 150iterations 3.0689065E-03 5.4885864E-02 at 160iterations 1.8143298E-03 3.2688141E-02 at 170iterations 1.0845074E-03 2.1175385E-02 at 180iterations finished qdiffx linear iterations at : 15:26:51 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 1.0845074E-03 2.1175385E-02 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.13000 DelPhi exited at 15:26:52 15.129u 0.302s 0:16.09 95.8% 0+0k 0+0io 0pf+0w