Sun Oct 9 19:04:24 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 19:04:24 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5191 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5500959 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): 3.272000 67.98800 ymin,ymax (A): -9.076000 53.29500 zmin,zma (A): -2.573000 61.51900 x,y,z range (A): 64.71600 62.37100 64.09200 scale (grids/A): 0.5500959 object centre (A): 35.63000 22.10950 29.47300 number of atom coordinates read : 5191 total number of charged atoms : 5043 net assigned charge : -0.9399430 assigned positive charge : 800.4514 centred at (gu) : 87.85105 89.33423 89.80164 assigned negative charge : -801.3976 centred at (gu) : 87.73219 89.36758 89.75839 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 10194 nv = 96 ne = 84 npr = 105684 no. pairs analyzed = 105684 no. exposed pairs = 5963 no. arc points = 40904 no. surface atoms = 2041 nbur = 3150 mkacc time = 0.2400000 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 = 1.540000 m= 457 mr = 5845 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4775 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4192 ## 465 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 13478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6446215E-10 5.3898130E-10 midg,1,midg; midg,igrid,midg 5.0976207E-10 -4.1900863E-10 1,midg,midg; igrid,midg,midg -2.9329132E-09 9.3700281E-10 gauss-seidel spectral radius is 0.9831178 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 19:04:25 rms-change max change #iterations 0.1077837 13.52745 at 10iterations 8.9206295E-03 1.308044 at 20iterations 2.1039157E-03 0.2535934 at 30iterations 9.0182398E-04 0.1044731 at 40iterations 4.1102301E-04 5.1369667E-02 at 50iterations finished qdiffx linear iterations at : 19:04:28 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 4.1102301E-04 5.1369667E-02 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 19:04:29 3.687u 0.134s 0:04.09 93.1% 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 Sun Oct 9 2011 at 19:04:29 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5191 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 1.650288 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): 3.272000 67.98800 ymin,ymax (A): -9.076000 53.29500 zmin,zma (A): -2.573000 61.51900 x,y,z range (A): 64.71600 62.37100 64.09200 scale (grids/A): 1.650288 object centre (A): 35.63000 22.10950 29.47300 number of atom coordinates read : 5191 total number of charged atoms : 5043 net assigned charge : -0.9399430 assigned positive charge : 800.4514 centred at (gu) : 83.55180 88.00114 89.40318 assigned negative charge : -801.3976 centred at (gu) : 83.19656 88.10275 89.27533 start vw surface at 0.3000000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 114039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40904 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38749 mr = 82835 m= 4482 mr = 28111 m= 142 mr = 2397 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 44051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 406 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 38700 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) : 0.5500959 object centre at (A) : 35.63000 22.10950 29.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0732498E-02 -1.5011579E-02 midg,1,midg; midg,igrid,midg 1.9955287E-02 7.4769324E-03 1,midg,midg; igrid,midg,midg -2.7792970E-02 1.5754921E-02 gauss-seidel spectral radius is 0.9984211 estimated iterations to convergence 200 setup time was (sec) 1.170000 now iterating at: 19:04:30 rms-change max change #iterations 4.853597 172.6715 at 10iterations 2.145721 66.54721 at 20iterations 0.9522919 27.58349 at 30iterations 0.4222909 12.67101 at 40iterations 0.1875200 5.179855 at 50iterations 8.3324939E-02 2.366699 at 60iterations 3.7161954E-02 1.095449 at 70iterations 1.6754474E-02 0.4505205 at 80iterations 7.7899857E-03 0.2183666 at 90iterations 3.8429149E-03 0.1018238 at 100iterations 2.1226711E-03 6.0851812E-02 at 110iterations 1.3453829E-03 3.6501884E-02 at 120iterations finished qdiffx linear iterations at : 19:04:37 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.3453829E-03 3.6501884E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 19:04:37 8.072u 0.182s 0:08.56 96.3% 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 Sun Oct 9 2011 at 19:04:37 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5191 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: SEP 674 has a net charge of -0.4750 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2100000 grid size : 179 scale,in grids/A, set to be: 2.475431 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): 3.272000 67.98800 ymin,ymax (A): -9.076000 53.29500 zmin,zma (A): -2.573000 61.51900 x,y,z range (A): 64.71600 62.37100 64.09200 scale (grids/A): 2.475431 object centre (A): 35.63000 22.10950 29.47300 number of atom coordinates read : 5191 total number of charged atoms : 5043 net assigned charge : -0.9399430 assigned positive charge : 800.4514 centred at (gu) : 80.32719 87.00162 89.10458 assigned negative charge : -801.3976 centred at (gu) : 79.79466 87.15388 88.91298 start vw surface at 0.2900000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 265208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40904 grid for indexing accessible points = 1.400000 m= 132132 mr = 201541 m= 40736 mr = 107921 m= 7324 mr = 31708 m= 652 mr = 5043 m= 14 mr = 318 m= 0 mr = 4 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.080000 number of dielectric boundary points 99531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 40291 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) : 1.650288 object centre at (A) : 35.63000 22.10950 29.47300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3323848 -0.3375707 midg,1,midg; midg,igrid,midg 0.1260241 -5.7732247E-02 1,midg,midg; igrid,midg,midg -0.4856757 0.2263799 gauss-seidel spectral radius is 0.9992503 estimated iterations to convergence 288 setup time was (sec) 2.390000 now iterating at: 19:04:40 rms-change max change #iterations 12.35170 341.8935 at 10iterations 7.282061 153.0701 at 20iterations 4.263569 77.36797 at 30iterations 2.485062 45.67905 at 40iterations 1.442711 26.84175 at 50iterations 0.8368716 14.67385 at 60iterations 0.4829564 8.835686 at 70iterations 0.2789373 4.532894 at 80iterations 0.1610279 2.680573 at 90iterations 9.2787661E-02 1.537533 at 100iterations 5.3370915E-02 0.8145638 at 110iterations 3.0833406E-02 0.5053749 at 120iterations 1.7880274E-02 0.3157582 at 130iterations 1.0465796E-02 0.1796436 at 140iterations 6.2482436E-03 0.1205597 at 150iterations 3.8639302E-03 7.1830750E-02 at 160iterations 2.5209694E-03 5.0733805E-02 at 170iterations 1.7621819E-03 3.2894135E-02 at 180iterations finished qdiffx linear iterations at : 19:04:50 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.7621819E-03 3.2894135E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 19:04:51 13.220u 0.192s 0:13.68 98.0% 0+0k 0+0io 0pf+0w