Mon Oct 10 10:31:57 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 Mon Oct 10 2011 at 10:31:57 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2883 !!! WARNING: HIT 232 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5546122 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): 18.05900 82.24800 ymin,ymax (A): 30.76000 89.24700 zmin,zma (A): -1.948000 50.56900 x,y,z range (A): 64.18900 58.48700 52.51700 scale (grids/A): 0.5546122 object centre (A): 50.15350 60.00350 24.31050 number of atom coordinates read : 2883 total number of charged atoms : 2731 net assigned charge : 6.014013 assigned positive charge : 426.4308 centred at (gu) : 87.95798 88.64957 86.77968 assigned negative charge : -420.4173 centred at (gu) : 87.85439 88.63139 86.71407 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6087 nv = 96 ne = 84 npr = 55517 no. pairs analyzed = 55517 no. exposed pairs = 4244 no. arc points = 30722 no. surface atoms = 1411 nbur = 1472 mkacc time = 0.1300000 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 = 1.540000 m= 299 mr = 2798 m= 0 mr = 11 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2965 ## 358 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3082153E-11 5.1296217E-10 midg,1,midg; midg,igrid,midg 5.5050986E-10 5.1344334E-10 1,midg,midg; igrid,midg,midg -5.7397143E-10 8.6714802E-10 gauss-seidel spectral radius is 0.9832427 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 10:31:57 rms-change max change #iterations 8.0786623E-02 15.55638 at 10iterations 5.5155950E-03 1.064259 at 20iterations 3.9567283E-04 5.8208466E-02 at 30iterations 3.5338657E-05 5.6886673E-03 at 40iterations 5.3647459E-06 6.2561035E-04 at 50iterations finished qdiffx linear iterations at : 10:32:00 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 5.3647459E-06 6.2561035E-04 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 10:32:01 3.581u 0.179s 0:04.05 92.5% 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 Mon Oct 10 2011 at 10:32:01 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2883 !!! WARNING: HIT 232 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.663836 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): 18.05900 82.24800 ymin,ymax (A): 30.76000 89.24700 zmin,zma (A): -1.948000 50.56900 x,y,z range (A): 64.18900 58.48700 52.51700 scale (grids/A): 1.663836 object centre (A): 50.15350 60.00350 24.31050 number of atom coordinates read : 2883 total number of charged atoms : 2731 net assigned charge : 6.014013 assigned positive charge : 426.4308 centred at (gu) : 83.87312 85.94815 80.33844 assigned negative charge : -420.4173 centred at (gu) : 83.56290 85.89370 80.14188 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30722 grid for indexing accessible points = 1.400000 m= 19909 mr = 41690 m= 2302 mr = 12576 m= 76 mr = 1002 m= 1 mr = 6 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 0.5200000 number of dielectric boundary points 33088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 339 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 21046 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) : 0.5546122 object centre at (A) : 50.15350 60.00350 24.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1265470E-05 4.6230648E-03 midg,1,midg; midg,igrid,midg 4.6661398E-03 1.2127465E-02 1,midg,midg; igrid,midg,midg -1.7194383E-02 -8.8655669E-03 gauss-seidel spectral radius is 0.9982542 estimated iterations to convergence 190 setup time was (sec) 0.8300000 now iterating at: 10:32:02 rms-change max change #iterations 3.369298 170.8372 at 10iterations 1.423461 63.23733 at 20iterations 0.5996186 21.13995 at 30iterations 0.2540029 8.865433 at 40iterations 0.1072578 3.806870 at 50iterations 4.5242865E-02 1.778428 at 60iterations 1.9103566E-02 0.6633949 at 70iterations 8.0908341E-03 0.2945214 at 80iterations 3.4229327E-03 0.1286983 at 90iterations 1.4529285E-03 5.0926208E-02 at 100iterations 6.1546353E-04 2.1258354E-02 at 110iterations 2.6073697E-04 1.1016846E-02 at 120iterations finished qdiffx linear iterations at : 10:32:09 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.6073697E-04 1.1016846E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 10:32:09 7.922u 0.217s 0:08.41 96.6% 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 Mon Oct 10 2011 at 10:32:09 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2883 !!! WARNING: HIT 232 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.495755 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): 18.05900 82.24800 ymin,ymax (A): 30.76000 89.24700 zmin,zma (A): -1.948000 50.56900 x,y,z range (A): 64.18900 58.48700 52.51700 scale (grids/A): 2.495755 object centre (A): 50.15350 60.00350 24.31050 number of atom coordinates read : 2883 total number of charged atoms : 2731 net assigned charge : 6.014013 assigned positive charge : 426.4308 centred at (gu) : 80.80958 83.92213 75.50758 assigned negative charge : -420.4173 centred at (gu) : 80.34420 83.84048 75.21266 start vw surface at 0.1700000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 153711 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30722 grid for indexing accessible points = 1.400000 m= 67986 mr = 103371 m= 19885 mr = 51120 m= 3449 mr = 13952 m= 291 mr = 2050 m= 9 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 74706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 21828 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) : 1.663836 object centre at (A) : 50.15350 60.00350 24.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2980545E-02 5.4483533E-02 midg,1,midg; midg,igrid,midg 2.4326444E-02 0.1750674 1,midg,midg; igrid,midg,midg -0.4907778 -0.3048512 gauss-seidel spectral radius is 0.9991636 estimated iterations to convergence 273 setup time was (sec) 1.580000 now iterating at: 10:32:11 rms-change max change #iterations 8.908682 285.2003 at 10iterations 5.146767 152.7364 at 20iterations 2.944712 95.04398 at 30iterations 1.666432 57.60043 at 40iterations 0.9421804 27.54140 at 50iterations 0.5273744 15.55291 at 60iterations 0.2958545 9.605028 at 70iterations 0.1651202 4.205834 at 80iterations 9.2056751E-02 3.288521 at 90iterations 5.1322885E-02 1.264835 at 100iterations 2.8581884E-02 0.7180252 at 110iterations 1.5867401E-02 0.3922327 at 120iterations 8.8636354E-03 0.1938477 at 130iterations 4.9111284E-03 0.1214924 at 140iterations 2.7226766E-03 6.0590267E-02 at 150iterations 1.5152238E-03 3.2826424E-02 at 160iterations 8.4236520E-04 2.0723820E-02 at 170iterations 4.6664337E-04 1.0627747E-02 at 180iterations finished qdiffx linear iterations at : 10:32:23 total time elapsed so far: 13.73000 # loops : 180 mean,max change (kT/e) : 4.6664337E-04 1.0627747E-02 energy calculations done at 13.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.92000 DelPhi exited at 10:32:24 13.918u 0.238s 0:14.46 97.7% 0+0k 0+0io 0pf+0w