Sat Oct 15 13:55:33 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 13:55:33 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1832 !!! WARNING: HIZ 63 has a net charge of 0.2000 !!! WARNING: HIZ 78 has a net charge of 0.2000 !!! WARNING: HIY 91 has a net charge of 0.2000 !!! WARNING: HIZ 113 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 222 has a net charge of 0.2000 !!! WARNING: HIZ 237 has a net charge of 0.2000 !!! WARNING: HIY 250 has a net charge of 0.2000 !!! WARNING: ZN3 320 has a net charge of 1.4000 !!! WARNING: ZN3 322 has a net charge of 1.4000 !!! WARNING: ZN3 323 has a net charge of 1.4000 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: 0.6436332 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): -27.20900 28.10200 ymin,ymax (A): -3.126000 37.98000 zmin,zma (A): 30.25800 75.41199 x,y,z range (A): 55.31100 41.10600 45.15399 scale (grids/A): 0.6436332 object centre (A): 0.4465008 17.42700 52.83500 number of atom coordinates read : 1832 total number of charged atoms : 1703 net assigned charge : -3.499991 assigned positive charge : 265.0845 centred at (gu) : 86.90903 90.01507 90.30889 assigned negative charge : -268.5843 centred at (gu) : 87.05326 90.14270 90.48426 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4936 nv = 96 ne = 84 npr = 38998 no. pairs analyzed = 38998 no. exposed pairs = 2424 no. arc points = 17243 no. surface atoms = 822 nbur = 1010 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 209 mr = 2424 m= 0 mr = 7 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2800000 number of dielectric boundary points 2714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1553 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 5855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6124148E-09 -2.3194534E-08 midg,1,midg; midg,igrid,midg 5.1369704E-09 -1.7412196E-08 1,midg,midg; igrid,midg,midg 1.3435071E-08 -9.8631308E-09 gauss-seidel spectral radius is 0.9874274 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 13:55:35 rms-change max change #iterations 0.1368752 30.52306 at 10iterations 1.3551841E-02 2.085489 at 20iterations 1.2927107E-03 0.2345390 at 30iterations 1.3256249E-04 2.1383286E-02 at 40iterations 1.3251999E-05 2.1572113E-03 at 50iterations finished qdiffx linear iterations at : 13:55:40 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.3251999E-05 2.1572113E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 13:55:40 4.091u 0.402s 0:07.06 63.5% 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 13:55:41 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1832 !!! WARNING: HIZ 63 has a net charge of 0.2000 !!! WARNING: HIZ 78 has a net charge of 0.2000 !!! WARNING: HIY 91 has a net charge of 0.2000 !!! WARNING: HIZ 113 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 222 has a net charge of 0.2000 !!! WARNING: HIZ 237 has a net charge of 0.2000 !!! WARNING: HIY 250 has a net charge of 0.2000 !!! WARNING: ZN3 320 has a net charge of 1.4000 !!! WARNING: ZN3 322 has a net charge of 1.4000 !!! WARNING: ZN3 323 has a net charge of 1.4000 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: 1.930900 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): -27.20900 28.10200 ymin,ymax (A): -3.126000 37.98000 zmin,zma (A): 30.25800 75.41199 x,y,z range (A): 55.31100 41.10600 45.15399 scale (grids/A): 1.930900 object centre (A): 0.4465008 17.42700 52.83500 number of atom coordinates read : 1832 total number of charged atoms : 1703 net assigned charge : -3.499991 assigned positive charge : 265.0845 centred at (gu) : 80.72743 90.04564 90.92673 assigned negative charge : -268.5843 centred at (gu) : 81.15994 90.42828 91.45295 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 53100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17243 grid for indexing accessible points = 1.400000 m= 16256 mr = 34178 m= 2200 mr = 11093 m= 128 mr = 1239 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 429 time to turn everything in is 0.4200000 number of dielectric boundary points 25141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 13424 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) : 0.6436332 object centre at (A) : 0.4465008 17.42700 52.83500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4291679E-02 -2.9304290E-02 midg,1,midg; midg,igrid,midg 5.9878727E-04 -9.2054959E-03 1,midg,midg; igrid,midg,midg 2.6578916E-02 -1.2909473E-02 gauss-seidel spectral radius is 0.9985949 estimated iterations to convergence 211 setup time was (sec) 0.7000000 now iterating at: 13:55:43 rms-change max change #iterations 3.603578 180.2120 at 10iterations 1.668339 62.27243 at 20iterations 0.7694387 28.55005 at 30iterations 0.3559563 13.16986 at 40iterations 0.1643124 6.137367 at 50iterations 7.5893998E-02 2.631495 at 60iterations 3.5097886E-02 1.230728 at 70iterations 1.6201939E-02 0.5641079 at 80iterations 7.5046211E-03 0.2810526 at 90iterations 3.4737892E-03 0.1424408 at 100iterations 1.6114397E-03 6.8511963E-02 at 110iterations 7.4393657E-04 3.0336380E-02 at 120iterations finished qdiffx linear iterations at : 13:55:57 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 7.4393657E-04 3.0336380E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 13:55:57 9.539u 0.477s 0:16.95 58.9% 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 Sat Oct 15 2011 at 13:55:58 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1832 !!! WARNING: HIZ 63 has a net charge of 0.2000 !!! WARNING: HIZ 78 has a net charge of 0.2000 !!! WARNING: HIY 91 has a net charge of 0.2000 !!! WARNING: HIZ 113 has a net charge of 0.2000 !!! WARNING: HIZ 117 has a net charge of 0.2000 !!! WARNING: HIZ 123 has a net charge of 0.2000 !!! WARNING: HIZ 222 has a net charge of 0.2000 !!! WARNING: HIZ 237 has a net charge of 0.2000 !!! WARNING: HIY 250 has a net charge of 0.2000 !!! WARNING: ZN3 320 has a net charge of 1.4000 !!! WARNING: ZN3 322 has a net charge of 1.4000 !!! WARNING: ZN3 323 has a net charge of 1.4000 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: 2.896350 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): -27.20900 28.10200 ymin,ymax (A): -3.126000 37.98000 zmin,zma (A): 30.25800 75.41199 x,y,z range (A): 55.31100 41.10600 45.15399 scale (grids/A): 2.896350 object centre (A): 0.4465008 17.42700 52.83500 number of atom coordinates read : 1832 total number of charged atoms : 1703 net assigned charge : -3.499991 assigned positive charge : 265.0845 centred at (gu) : 76.09126 90.06845 91.39033 assigned negative charge : -268.5843 centred at (gu) : 76.73990 90.64243 92.17941 start vw surface at 0.1100000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 122754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17243 grid for indexing accessible points = 1.400000 m= 54092 mr = 83476 m= 17279 mr = 42210 m= 3872 mr = 13260 m= 526 mr = 2699 m= 22 mr = 288 m= 0 mr = 12 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1450 time to turn everything in is 1.100000 number of dielectric boundary points 56600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 13624 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) : 1.930900 object centre at (A) : 0.4465008 17.42700 52.83500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1714714 -0.3100481 midg,1,midg; midg,igrid,midg -7.7218465E-03 -5.2032530E-02 1,midg,midg; igrid,midg,midg 5.3408444E-02 -8.9088872E-02 gauss-seidel spectral radius is 0.9992478 estimated iterations to convergence 288 setup time was (sec) 1.470000 now iterating at: 13:55:59 rms-change max change #iterations 8.417899 324.6302 at 10iterations 4.849368 133.6163 at 20iterations 2.791721 66.84430 at 30iterations 1.600598 39.51267 at 40iterations 0.9158328 24.23755 at 50iterations 0.5227825 11.08199 at 60iterations 0.2984853 6.325521 at 70iterations 0.1702245 4.420299 at 80iterations 9.7439177E-02 2.338350 at 90iterations 5.5610780E-02 1.298615 at 100iterations 3.1719152E-02 0.6976776 at 110iterations 1.8075028E-02 0.3547592 at 120iterations 1.0295655E-02 0.2110219 at 130iterations 5.8687665E-03 0.1294112 at 140iterations 3.3521808E-03 6.6787720E-02 at 150iterations 1.9109948E-03 4.0508270E-02 at 160iterations 1.0928976E-03 2.2792816E-02 at 170iterations 6.2306575E-04 1.2441635E-02 at 180iterations finished qdiffx linear iterations at : 13:56:13 total time elapsed so far: 15.04000 # loops : 180 mean,max change (kT/e) : 6.2306575E-04 1.2441635E-02 energy calculations done at 15.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.21000 DelPhi exited at 13:56:13 15.219u 0.463s 0:15.94 98.3% 0+0k 0+0io 0pf+0w