Mon Oct 10 12:22:37 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 Mon Oct 10 2011 at 12:22:37 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7410799 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): 42.78200 90.33100 ymin,ymax (A): 7.940000 54.18400 zmin,zma (A): 5.501000 53.53900 x,y,z range (A): 47.54900 46.24400 48.03800 scale (grids/A): 0.7410799 object centre (A): 66.55650 31.06200 29.52000 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 89.29897 89.52193 90.39593 assigned negative charge : -320.7320 centred at (gu) : 89.28951 89.48772 90.24298 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7964 nv = 96 ne = 84 npr = 43111 no. pairs analyzed = 43111 no. exposed pairs = 2686 no. arc points = 18592 no. surface atoms = 914 nbur = 1193 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4457 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2600000 number of dielectric boundary points 3937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1458 ## 123 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8366 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3851683E-07 6.6775371E-08 midg,1,midg; midg,igrid,midg -1.4311699E-07 -5.5149719E-08 1,midg,midg; igrid,midg,midg -1.1952444E-07 -7.5512801E-08 gauss-seidel spectral radius is 0.9905115 estimated iterations to convergence 83 setup time was (sec) 0.5500000 now iterating at: 12:22:38 rms-change max change #iterations 0.2525214 37.59596 at 10iterations 3.4354825E-02 4.793849 at 20iterations 4.5099850E-03 0.5651646 at 30iterations 6.2155334E-04 9.2220306E-02 at 40iterations 8.2870974E-05 1.1657715E-02 at 50iterations finished qdiffx linear iterations at : 12:22:42 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 8.2870974E-05 1.1657715E-02 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 12:22:43 4.507u 0.401s 0:05.32 92.1% 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 Mon Oct 10 2011 at 12:22:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.223240 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): 42.78200 90.33100 ymin,ymax (A): 7.940000 54.18400 zmin,zma (A): 5.501000 53.53900 x,y,z range (A): 47.54900 46.24400 48.03800 scale (grids/A): 2.223240 object centre (A): 66.55650 31.06200 29.52000 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 87.89688 88.56567 91.18754 assigned negative charge : -320.7320 centred at (gu) : 87.86871 88.46317 90.72897 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83793 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18592 grid for indexing accessible points = 1.400000 m= 33451 mr = 57965 m= 7181 mr = 25509 m= 738 mr = 4996 m= 30 mr = 391 m= 0 mr = 7 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 361 time to turn everything in is 0.7000000 number of dielectric boundary points 36325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15687 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) : 0.7410799 object centre at (A) : 66.55650 31.06200 29.52000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1041124 7.8718783E-03 midg,1,midg; midg,igrid,midg -3.7218396E-02 -3.0663472E-02 1,midg,midg; igrid,midg,midg -9.1611883E-03 7.1174190E-03 gauss-seidel spectral radius is 0.9989281 estimated iterations to convergence 242 setup time was (sec) 1.010000 now iterating at: 12:22:44 rms-change max change #iterations 5.131141 223.1456 at 10iterations 2.608836 84.04279 at 20iterations 1.326277 36.49533 at 30iterations 0.6776222 19.27733 at 40iterations 0.3449527 10.91145 at 50iterations 0.1763877 5.016133 at 60iterations 8.9984365E-02 2.609692 at 70iterations 4.5920599E-02 1.324150 at 80iterations 2.3388851E-02 0.6631851 at 90iterations 1.1970019E-02 0.3424425 at 100iterations 6.0873022E-03 0.1885872 at 110iterations 3.1182186E-03 0.1008301 at 120iterations finished qdiffx linear iterations at : 12:22:54 total time elapsed so far: 11.23000 # loops : 120 mean,max change (kT/e) : 3.1182186E-03 0.1008301 energy calculations done at 11.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 12:22:55 11.386u 0.445s 0:12.28 96.2% 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 12:22:55 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2107 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.334860 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): 42.78200 90.33100 ymin,ymax (A): 7.940000 54.18400 zmin,zma (A): 5.501000 53.53900 x,y,z range (A): 47.54900 46.24400 48.03800 scale (grids/A): 3.334860 object centre (A): 66.55650 31.06200 29.52000 number of atom coordinates read : 2107 total number of charged atoms : 1969 net assigned charge : -5.271990 assigned positive charge : 315.4599 centred at (gu) : 86.84538 87.84843 91.78122 assigned negative charge : -320.7320 centred at (gu) : 86.80296 87.69482 91.09335 start vw surface at 0.1000000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 193263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18592 grid for indexing accessible points = 1.400000 m= 102494 mr = 140042 m= 43782 mr = 84826 m= 13585 mr = 36290 m= 3009 mr = 10914 m= 372 mr = 2307 m= 22 mr = 239 m= 0 mr = 16 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 1137 time to turn everything in is 2.180000 number of dielectric boundary points 81893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.310000 number of grid points assigned charge 15752 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) : 2.223240 object centre at (A) : 66.55650 31.06200 29.52000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.057314 0.1742534 midg,1,midg; midg,igrid,midg -0.2024456 -0.2598226 1,midg,midg; igrid,midg,midg -0.1424615 -1.3971295E-02 gauss-seidel spectral radius is 0.9993182 estimated iterations to convergence 302 setup time was (sec) 2.520000 now iterating at: 12:22:58 rms-change max change #iterations 10.97127 330.8450 at 10iterations 6.445294 111.6829 at 20iterations 3.799484 64.88280 at 30iterations 2.230430 41.29264 at 40iterations 1.310603 23.11467 at 50iterations 0.7708136 11.57554 at 60iterations 0.4516886 7.594970 at 70iterations 0.2652191 4.277532 at 80iterations 0.1555133 2.416367 at 90iterations 9.1630541E-02 1.515730 at 100iterations 5.3568624E-02 0.8552246 at 110iterations 3.1456135E-02 0.5718555 at 120iterations 1.8465124E-02 0.2996585 at 130iterations 1.0837466E-02 0.1878452 at 140iterations 6.3528134E-03 0.1036189 at 150iterations 3.7259394E-03 6.0968876E-02 at 160iterations 2.1919785E-03 3.5882950E-02 at 170iterations 1.2876955E-03 1.9554138E-02 at 180iterations finished qdiffx linear iterations at : 12:23:15 total time elapsed so far: 19.29000 # loops : 180 mean,max change (kT/e) : 1.2876955E-03 1.9554138E-02 energy calculations done at 19.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.46000 DelPhi exited at 12:23:15 19.465u 0.467s 0:20.24 98.4% 0+0k 0+0io 0pf+0w