Wed Dec 21 14:22:12 PST 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 Wed Dec 21 2011 at 14:22:14 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASH 122 has a net charge of -0.3190 !!! WARNING: GLM 197 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: 0.6110644 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): -23.68800 34.57100 ymin,ymax (A): -18.36000 20.52300 zmin,zma (A): -3.689000 38.37000 x,y,z range (A): 58.25900 38.88300 42.05900 scale (grids/A): 0.6110644 object centre (A): 5.441502 1.081500 17.34050 number of atom coordinates read : 1990 total number of charged atoms : 1853 net assigned charge : 1.587007 assigned positive charge : 294.4140 centred at (gu) : 89.83337 90.01478 90.24418 assigned negative charge : -292.8273 centred at (gu) : 89.85049 90.10973 90.40965 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5083 nv = 96 ne = 84 npr = 39669 no. pairs analyzed = 39669 no. exposed pairs = 2618 no. arc points = 18004 no. surface atoms = 892 nbur = 1098 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 259 mr = 2664 m= 0 mr = 20 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1822 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6064 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8693731E-09 -5.8298038E-09 midg,1,midg; midg,igrid,midg 4.6016937E-09 -2.7179015E-09 1,midg,midg; igrid,midg,midg 1.7150431E-09 3.2126857E-10 gauss-seidel spectral radius is 0.9860852 estimated iterations to convergence 69 setup time was (sec) 0.7300000 now iterating at: 14:22:16 rms-change max change #iterations 0.1032668 19.20882 at 10iterations 8.9932233E-03 1.593857 at 20iterations 7.9395925E-04 0.1301756 at 30iterations 6.9779227E-05 1.1283875E-02 at 40iterations 6.1760916E-06 9.1648102E-04 at 50iterations finished qdiffx linear iterations at : 14:22:24 total time elapsed so far: 8.300000 # loops : 50 mean,max change (kT/e) : 6.1760916E-06 9.1648102E-04 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.470000 DelPhi exited at 14:22:29 8.476u 0.715s 0:16.45 55.8% 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 Wed Dec 21 2011 at 14:22:33 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASH 122 has a net charge of -0.3190 !!! WARNING: GLM 197 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.833193 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): -23.68800 34.57100 ymin,ymax (A): -18.36000 20.52300 zmin,zma (A): -3.689000 38.37000 x,y,z range (A): 58.25900 38.88300 42.05900 scale (grids/A): 1.833193 object centre (A): 5.441502 1.081500 17.34050 number of atom coordinates read : 1990 total number of charged atoms : 1853 net assigned charge : 1.587007 assigned positive charge : 294.4140 centred at (gu) : 89.50014 90.04437 90.73262 assigned negative charge : -292.8273 centred at (gu) : 89.55173 90.32937 91.22928 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 54134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18004 grid for indexing accessible points = 1.400000 m= 19683 mr = 36424 m= 2845 mr = 14421 m= 118 mr = 1687 m= 2 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 24220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14532 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) : 0.6110644 object centre at (A) : 5.441502 1.081500 17.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0179032E-03 -9.6541420E-03 midg,1,midg; midg,igrid,midg 1.7908238E-03 -4.7797770E-03 1,midg,midg; igrid,midg,midg 4.3502755E-02 3.4056544E-02 gauss-seidel spectral radius is 0.9984602 estimated iterations to convergence 202 setup time was (sec) 0.7500000 now iterating at: 14:22:35 rms-change max change #iterations 3.360587 159.7776 at 10iterations 1.492000 58.58570 at 20iterations 0.6668806 26.99814 at 30iterations 0.2969346 11.02276 at 40iterations 0.1319882 5.268555 at 50iterations 5.9235215E-02 2.421071 at 60iterations 2.6364354E-02 0.9974813 at 70iterations 1.1757902E-02 0.4191358 at 80iterations 5.2314969E-03 0.1947098 at 90iterations 2.3492433E-03 8.4501266E-02 at 100iterations 1.0465593E-03 3.6751270E-02 at 110iterations 4.6836326E-04 1.9273758E-02 at 120iterations finished qdiffx linear iterations at : 14:22:49 total time elapsed so far: 14.99000 # loops : 120 mean,max change (kT/e) : 4.6836326E-04 1.9273758E-02 energy calculations done at 14.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.16000 DelPhi exited at 14:22:58 15.161u 0.480s 0:25.49 61.3% 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 Wed Dec 21 2011 at 14:23:00 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1990 !!! WARNING: ASH 122 has a net charge of -0.3190 !!! WARNING: GLM 197 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: 2.749790 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): -23.68800 34.57100 ymin,ymax (A): -18.36000 20.52300 zmin,zma (A): -3.689000 38.37000 x,y,z range (A): 58.25900 38.88300 42.05900 scale (grids/A): 2.749790 object centre (A): 5.441502 1.081500 17.34050 number of atom coordinates read : 1990 total number of charged atoms : 1853 net assigned charge : 1.587007 assigned positive charge : 294.4140 centred at (gu) : 89.25021 90.06648 91.09888 assigned negative charge : -292.8273 centred at (gu) : 89.32767 90.49395 91.84399 start vw surface at 0.1000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 124691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18004 grid for indexing accessible points = 1.400000 m= 63530 mr = 88163 m= 22735 mr = 51642 m= 4937 mr = 18102 m= 475 mr = 3612 m= 16 mr = 246 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.370000 number of dielectric boundary points 54616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14822 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) : 1.833193 object centre at (A) : 5.441502 1.081500 17.34050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7541502E-02 -9.3364269E-02 midg,1,midg; midg,igrid,midg -1.3257916E-02 -4.1319858E-02 1,midg,midg; igrid,midg,midg 0.5222917 0.4160977 gauss-seidel spectral radius is 0.9991961 estimated iterations to convergence 278 setup time was (sec) 1.960000 now iterating at: 14:23:03 rms-change max change #iterations 8.268450 333.2366 at 10iterations 4.778313 126.3516 at 20iterations 2.721847 68.67995 at 30iterations 1.554261 35.82997 at 40iterations 0.8802808 19.77587 at 50iterations 0.4981512 11.87594 at 60iterations 0.2814709 5.915638 at 70iterations 0.1585213 4.019595 at 80iterations 8.9289740E-02 1.794878 at 90iterations 5.0283566E-02 1.115375 at 100iterations 2.8222520E-02 0.5871792 at 110iterations 1.5884403E-02 0.3492165 at 120iterations 8.9418171E-03 0.1945630 at 130iterations 5.0099553E-03 0.1000843 at 140iterations 2.8092840E-03 5.8191419E-02 at 150iterations 1.5791337E-03 3.2751083E-02 at 160iterations 8.8556577E-04 1.8981934E-02 at 170iterations 4.9687602E-04 1.0399818E-02 at 180iterations finished qdiffx linear iterations at : 14:23:30 total time elapsed so far: 28.60000 # loops : 180 mean,max change (kT/e) : 4.9687602E-04 1.0399818E-02 energy calculations done at 28.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.79000 DelPhi exited at 14:23:30 28.794u 0.863s 0:30.35 97.6% 0+0k 0+0io 0pf+0w