Sun Oct 9 08:58:17 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 Sun Oct 9 2011 at 08:58:17 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5899 !!! WARNING: HIR 702 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4661455 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): 3.837000 80.20800 ymin,ymax (A): 22.53100 84.16100 zmin,zma (A): 6.315000 70.65500 x,y,z range (A): 76.37100 61.63000 64.34000 scale (grids/A): 0.4661455 object centre (A): 42.02250 53.34600 38.48500 number of atom coordinates read : 5899 total number of charged atoms : 5730 net assigned charge : -1.985959 assigned positive charge : 889.0173 centred at (gu) : 89.62888 88.87814 89.47962 assigned negative charge : -891.0109 centred at (gu) : 89.49761 88.86768 89.42503 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7824 nv = 96 ne = 84 npr = 118508 no. pairs analyzed = 118508 no. exposed pairs = 7470 no. arc points = 51959 no. surface atoms = 2494 nbur = 3405 mkacc time = 0.3200000 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 = 1.820000 m= 245 mr = 3883 m= 0 mr = 2 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.5800000 number of dielectric boundary points 4184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4729 ## 870 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 10776 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9035723E-11 1.6364783E-11 midg,1,midg; midg,igrid,midg -9.6745389E-12 1.0044660E-12 1,midg,midg; igrid,midg,midg -6.3191001E-11 4.4105615E-11 gauss-seidel spectral radius is 0.9765704 estimated iterations to convergence 54 setup time was (sec) 0.9500000 now iterating at: 08:58:18 rms-change max change #iterations 4.6750113E-02 7.042057 at 10iterations 2.1363590E-03 0.2875595 at 20iterations 1.6756672E-04 4.3788910E-02 at 30iterations 3.3665678E-05 9.2906952E-03 at 40iterations 8.6493255E-06 2.1839142E-03 at 50iterations finished qdiffx linear iterations at : 08:58:23 total time elapsed so far: 5.600000 # loops : 50 mean,max change (kT/e) : 8.6493255E-06 2.1839142E-03 energy calculations done at 5.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.770000 DelPhi exited at 08:58:23 5.770u 0.441s 0:06.49 95.6% 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 Sun Oct 9 2011 at 08:58:23 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5899 !!! WARNING: HIR 702 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.398437 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): 3.837000 80.20800 ymin,ymax (A): 22.53100 84.16100 zmin,zma (A): 6.315000 70.65500 x,y,z range (A): 76.37100 61.63000 64.34000 scale (grids/A): 1.398437 object centre (A): 42.02250 53.34600 38.48500 number of atom coordinates read : 5899 total number of charged atoms : 5730 net assigned charge : -1.985959 assigned positive charge : 889.0173 centred at (gu) : 88.88480 86.63285 88.43741 assigned negative charge : -891.0109 centred at (gu) : 88.49242 86.60254 88.27520 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 91578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51959 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 22186 mr = 61945 m= 1319 mr = 13600 m= 7 mr = 361 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 931 time to turn everything in is 0.7900000 number of dielectric boundary points 39184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 953 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 41502 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) : 0.4661455 object centre at (A) : 42.02250 53.34600 38.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8421273E-03 3.9234231E-03 midg,1,midg; midg,igrid,midg -1.2094774E-03 -2.3614138E-03 1,midg,midg; igrid,midg,midg -1.0220818E-02 1.3834234E-02 gauss-seidel spectral radius is 0.9977905 estimated iterations to convergence 169 setup time was (sec) 1.190000 now iterating at: 08:58:25 rms-change max change #iterations 3.446424 150.7007 at 10iterations 1.310519 44.78663 at 20iterations 0.5026011 16.03275 at 30iterations 0.1911885 6.830933 at 40iterations 7.3156580E-02 2.344299 at 50iterations 2.7958564E-02 0.8598471 at 60iterations 1.0679970E-02 0.3701248 at 70iterations 4.1004359E-03 0.1401911 at 80iterations 1.5768909E-03 5.3147316E-02 at 90iterations 6.0688198E-04 2.0897865E-02 at 100iterations 2.3726410E-04 9.6511841E-03 at 110iterations 9.4772724E-05 3.5247803E-03 at 120iterations finished qdiffx linear iterations at : 08:58:37 total time elapsed so far: 13.75000 # loops : 120 mean,max change (kT/e) : 9.4772724E-05 3.5247803E-03 energy calculations done at 13.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.92000 DelPhi exited at 08:58:38 13.923u 0.534s 0:14.92 96.8% 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 Sun Oct 9 2011 at 08:58:38 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5899 !!! WARNING: HIR 702 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.097655 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): 3.837000 80.20800 ymin,ymax (A): 22.53100 84.16100 zmin,zma (A): 6.315000 70.65500 x,y,z range (A): 76.37100 61.63000 64.34000 scale (grids/A): 2.097655 object centre (A): 42.02250 53.34600 38.48500 number of atom coordinates read : 5899 total number of charged atoms : 5730 net assigned charge : -1.985959 assigned positive charge : 889.0173 centred at (gu) : 88.32697 84.94856 87.65559 assigned negative charge : -891.0109 centred at (gu) : 87.73864 84.90367 87.41282 start vw surface at 0.2200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 214531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51959 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 85750 mr = 153933 m= 16602 mr = 64300 m= 1533 mr = 10921 m= 46 mr = 794 m= 0 mr = 7 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 3444 time to turn everything in is 1.890000 number of dielectric boundary points 88507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 45513 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) : 1.398437 object centre at (A) : 42.02250 53.34600 38.48500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6208371E-02 9.4117381E-02 midg,1,midg; midg,igrid,midg -2.0378241E-02 -4.0282615E-02 1,midg,midg; igrid,midg,midg -7.7539749E-02 0.2698316 gauss-seidel spectral radius is 0.9990946 estimated iterations to convergence 263 setup time was (sec) 2.310000 now iterating at: 08:58:41 rms-change max change #iterations 10.03419 309.1645 at 10iterations 5.652936 141.8208 at 20iterations 3.168151 82.18005 at 30iterations 1.762398 39.34560 at 40iterations 0.9806975 20.83575 at 50iterations 0.5403987 13.02868 at 60iterations 0.2985543 6.887522 at 70iterations 0.1640323 3.360129 at 80iterations 8.9917541E-02 2.081184 at 90iterations 4.9402423E-02 1.255874 at 100iterations 2.6969744E-02 0.5648079 at 110iterations 1.4759742E-02 0.2702560 at 120iterations 8.0538597E-03 0.1535568 at 130iterations 4.3988698E-03 8.6326599E-02 at 140iterations 2.4049212E-03 4.6398163E-02 at 150iterations 1.3096823E-03 2.6054382E-02 at 160iterations 7.1669638E-04 1.3602257E-02 at 170iterations 3.9132166E-04 7.8449249E-03 at 180iterations finished qdiffx linear iterations at : 08:59:01 total time elapsed so far: 21.98000 # loops : 180 mean,max change (kT/e) : 3.9132166E-04 7.8449249E-03 energy calculations done at 21.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.15000 DelPhi exited at 08:59:01 22.155u 0.531s 0:23.05 98.3% 0+0k 0+0io 0pf+0w