Sat Oct 8 15:47:48 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 15:47:48 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 = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6421125 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): -1.990000 47.45200 ymin,ymax (A): -17.46700 30.28700 zmin,zma (A): -19.12500 36.31700 x,y,z range (A): 49.44200 47.75400 55.44200 scale (grids/A): 0.6421125 object centre (A): 22.73100 6.409999 8.595999 number of atom coordinates read : 2377 total number of charged atoms : 2312 net assigned charge : 7.000003 assigned positive charge : 355.5941 centred at (gu) : 90.48798 89.10010 90.32619 assigned negative charge : -348.5948 centred at (gu) : 90.44141 89.19460 90.31449 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6889 nv = 96 ne = 84 npr = 46015 no. pairs analyzed = 46015 no. exposed pairs = 3192 no. arc points = 22257 no. surface atoms = 1074 nbur = 1303 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3702 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7819387E-09 1.2818340E-08 midg,1,midg; midg,igrid,midg 2.5502224E-08 1.7207540E-10 1,midg,midg; igrid,midg,midg 4.9959969E-09 1.7533432E-08 gauss-seidel spectral radius is 0.9874206 estimated iterations to convergence 73 setup time was (sec) 0.7100000 now iterating at: 15:47:49 rms-change max change #iterations 0.1365951 19.67846 at 10iterations 1.3697086E-02 1.945008 at 20iterations 1.5053368E-03 0.2090907 at 30iterations 2.5925579E-04 3.6209106E-02 at 40iterations 7.4021962E-05 1.1081696E-02 at 50iterations finished qdiffx linear iterations at : 15:47:53 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 7.4021962E-05 1.1081696E-02 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 15:47:53 4.476u 0.399s 0:05.16 94.1% 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 15:47:53 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 = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.926337 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): -1.990000 47.45200 ymin,ymax (A): -17.46700 30.28700 zmin,zma (A): -19.12500 36.31700 x,y,z range (A): 49.44200 47.75400 55.44200 scale (grids/A): 1.926337 object centre (A): 22.73100 6.409999 8.595999 number of atom coordinates read : 2377 total number of charged atoms : 2312 net assigned charge : 7.000003 assigned positive charge : 355.5941 centred at (gu) : 91.46362 87.29974 90.97794 assigned negative charge : -348.5948 centred at (gu) : 91.32407 87.58374 90.94331 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 73316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22257 grid for indexing accessible points = 1.400000 m= 27591 mr = 50563 m= 5270 mr = 20151 m= 379 mr = 3521 m= 5 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 32170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 18212 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) : 0.6421125 object centre at (A) : 22.73100 6.409999 8.595999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2418763E-02 -1.0336288E-02 midg,1,midg; midg,igrid,midg 2.6447065E-02 -1.9645994E-03 1,midg,midg; igrid,midg,midg 1.1800423E-02 -1.2181781E-02 gauss-seidel spectral radius is 0.9986541 estimated iterations to convergence 216 setup time was (sec) 1.080000 now iterating at: 15:47:55 rms-change max change #iterations 4.115762 160.8487 at 10iterations 1.934637 88.85007 at 20iterations 0.9081806 33.94621 at 30iterations 0.4297566 13.87162 at 40iterations 0.2023969 6.419150 at 50iterations 9.5210209E-02 3.238823 at 60iterations 4.4886988E-02 1.332932 at 70iterations 2.1142704E-02 0.6431160 at 80iterations 9.9947499E-03 0.3064378 at 90iterations 4.7514429E-03 0.1456928 at 100iterations 2.2627010E-03 7.5767517E-02 at 110iterations 1.0955987E-03 3.4679413E-02 at 120iterations finished qdiffx linear iterations at : 15:48:04 total time elapsed so far: 10.15000 # loops : 120 mean,max change (kT/e) : 1.0955987E-03 3.4679413E-02 energy calculations done at 10.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 15:48:04 10.375u 0.448s 0:11.13 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 15:48:04 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 = 2377 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.889506 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): -1.990000 47.45200 ymin,ymax (A): -17.46700 30.28700 zmin,zma (A): -19.12500 36.31700 x,y,z range (A): 49.44200 47.75400 55.44200 scale (grids/A): 2.889506 object centre (A): 22.73100 6.409999 8.595999 number of atom coordinates read : 2377 total number of charged atoms : 2312 net assigned charge : 7.000003 assigned positive charge : 355.5941 centred at (gu) : 92.19536 85.94952 91.46676 assigned negative charge : -348.5948 centred at (gu) : 91.98615 86.37547 91.41496 start vw surface at 0.1600000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 169506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22257 grid for indexing accessible points = 1.400000 m= 86938 mr = 122536 m= 34275 mr = 70539 m= 9870 mr = 27702 m= 1732 mr = 7782 m= 104 mr = 1257 m= 1 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 72547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 18495 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) : 1.926337 object centre at (A) : 22.73100 6.409999 8.595999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2632693 -0.2102269 midg,1,midg; midg,igrid,midg 0.1984172 -6.8039812E-02 1,midg,midg; igrid,midg,midg 0.1009071 -0.3598711 gauss-seidel spectral radius is 0.9992667 estimated iterations to convergence 291 setup time was (sec) 2.410000 now iterating at: 15:48:07 rms-change max change #iterations 9.746107 359.0673 at 10iterations 5.775660 131.0216 at 20iterations 3.398168 70.92012 at 30iterations 1.990740 41.07982 at 40iterations 1.162607 23.82378 at 50iterations 0.6788781 12.05084 at 60iterations 0.3946272 7.103444 at 70iterations 0.2288355 4.159231 at 80iterations 0.1326360 2.509737 at 90iterations 7.7021770E-02 1.445287 at 100iterations 4.4562034E-02 0.8870201 at 110iterations 2.5756244E-02 0.4913177 at 120iterations 1.4894995E-02 0.2594132 at 130iterations 8.5983137E-03 0.1633968 at 140iterations 4.9560270E-03 9.8031998E-02 at 150iterations 2.8653499E-03 5.2427292E-02 at 160iterations 1.6542643E-03 2.9733658E-02 at 170iterations 9.5291925E-04 1.6416550E-02 at 180iterations finished qdiffx linear iterations at : 15:48:23 total time elapsed so far: 17.92000 # loops : 180 mean,max change (kT/e) : 9.5291925E-04 1.6416550E-02 energy calculations done at 17.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.15000 DelPhi exited at 15:48:23 18.159u 0.452s 0:18.90 98.4% 0+0k 0+0io 0pf+0w