Mon Oct 10 17:03:56 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 Mon Oct 10 2011 at 17:03:56 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3602 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5813668 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): -29.94800 30.59600 ymin,ymax (A): -29.43600 31.79900 zmin,zma (A): 28.94200 86.25300 x,y,z range (A): 60.54400 61.23500 57.31100 scale (grids/A): 0.5813668 object centre (A): 0.3239994 1.181499 57.59750 number of atom coordinates read : 3602 total number of charged atoms : 3404 net assigned charge : 5.706038 assigned positive charge : 540.9481 centred at (gu) : 90.77789 91.30867 91.37321 assigned negative charge : -535.2437 centred at (gu) : 90.91524 91.34679 91.36799 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7855 nv = 96 ne = 84 npr = 73566 no. pairs analyzed = 73566 no. exposed pairs = 4600 no. arc points = 32315 no. surface atoms = 1550 nbur = 2052 mkacc time = 0.1700000 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 = 1.484000 m= 340 mr = 4099 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3305 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10085 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8758706E-10 2.0486126E-09 midg,1,midg; midg,igrid,midg 1.7753157E-09 3.7430356E-10 1,midg,midg; igrid,midg,midg 4.2351429E-09 -3.0285188E-09 gauss-seidel spectral radius is 0.9847772 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 17:03:57 rms-change max change #iterations 0.1090790 14.09297 at 10iterations 9.1204522E-03 1.361809 at 20iterations 1.2942367E-03 0.1925545 at 30iterations 3.8351939E-04 6.2660217E-02 at 40iterations 1.3295851E-04 2.2014618E-02 at 50iterations finished qdiffx linear iterations at : 17:04:00 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.3295851E-04 2.2014618E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 17:04:02 3.621u 0.178s 0:05.83 65.0% 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 17:04:02 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3602 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.744101 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): -29.94800 30.59600 ymin,ymax (A): -29.43600 31.79900 zmin,zma (A): 28.94200 86.25300 x,y,z range (A): 60.54400 61.23500 57.31100 scale (grids/A): 1.744101 object centre (A): 0.3239994 1.181499 57.59750 number of atom coordinates read : 3602 total number of charged atoms : 3404 net assigned charge : 5.706038 assigned positive charge : 540.9481 centred at (gu) : 92.33247 93.92555 94.11857 assigned negative charge : -535.2437 centred at (gu) : 92.74516 94.03995 94.10349 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 85587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32315 grid for indexing accessible points = 1.400000 m= 27971 mr = 57802 m= 3634 mr = 19583 m= 174 mr = 1908 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 555 time to turn everything in is 0.7200000 number of dielectric boundary points 38036 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 305 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 26420 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) : 0.5813668 object centre at (A) : 0.3239994 1.181499 57.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8401708E-03 3.6455160E-03 midg,1,midg; midg,igrid,midg 2.6753318E-02 -8.5408231E-03 1,midg,midg; igrid,midg,midg 2.6319705E-02 -4.4392943E-03 gauss-seidel spectral radius is 0.9984757 estimated iterations to convergence 203 setup time was (sec) 1.040000 now iterating at: 17:04:04 rms-change max change #iterations 4.264770 179.6636 at 10iterations 1.897987 58.10406 at 20iterations 0.8493976 26.12262 at 30iterations 0.3789725 11.17985 at 40iterations 0.1707564 5.327108 at 50iterations 7.6484017E-02 2.567827 at 60iterations 3.4446854E-02 1.064161 at 70iterations 1.5561393E-02 0.5080566 at 80iterations 7.0839613E-03 0.2163582 at 90iterations 3.2700226E-03 0.1000938 at 100iterations 1.5562120E-03 5.0180435E-02 at 110iterations 7.7962433E-04 2.7999878E-02 at 120iterations finished qdiffx linear iterations at : 17:04:11 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 7.7962433E-04 2.7999878E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 17:04:11 8.236u 0.258s 0:08.87 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 Mon Oct 10 2011 at 17:04:11 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3602 !!! WARNING: GLM 478 has a net charge of -0.0940 !!! WARNING: HEM 900 has a net charge of 1.4000 !!! WARNING: ZN9 951 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.616151 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): -29.94800 30.59600 ymin,ymax (A): -29.43600 31.79900 zmin,zma (A): 28.94200 86.25300 x,y,z range (A): 60.54400 61.23500 57.31100 scale (grids/A): 2.616151 object centre (A): 0.3239994 1.181499 57.59750 number of atom coordinates read : 3602 total number of charged atoms : 3404 net assigned charge : 5.706038 assigned positive charge : 540.9481 centred at (gu) : 93.49836 95.88811 96.17758 assigned negative charge : -535.2437 centred at (gu) : 94.11779 96.05987 96.15502 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 198368 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32315 grid for indexing accessible points = 1.400000 m= 94392 mr = 141422 m= 29661 mr = 74849 m= 5945 mr = 22636 m= 660 mr = 4046 m= 33 mr = 371 m= 0 mr = 6 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 2000 time to turn everything in is 1.690000 number of dielectric boundary points 85729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 27225 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) : 1.744101 object centre at (A) : 0.3239994 1.181499 57.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1291258E-02 8.7403178E-02 midg,1,midg; midg,igrid,midg 0.8567806 -0.1218029 1,midg,midg; igrid,midg,midg 0.3184751 -4.2855427E-02 gauss-seidel spectral radius is 0.9992375 estimated iterations to convergence 286 setup time was (sec) 2.060000 now iterating at: 17:04:14 rms-change max change #iterations 10.59728 331.8175 at 10iterations 6.191587 156.1957 at 20iterations 3.586252 79.88287 at 30iterations 2.073986 44.63026 at 40iterations 1.194976 26.49821 at 50iterations 0.6873740 13.85027 at 60iterations 0.3949303 8.818177 at 70iterations 0.2260008 4.603790 at 80iterations 0.1295651 2.331528 at 90iterations 7.4287593E-02 1.488951 at 100iterations 4.2543080E-02 0.8497162 at 110iterations 2.4341332E-02 0.4332924 at 120iterations 1.3914130E-02 0.2953663 at 130iterations 7.9988139E-03 0.1484461 at 140iterations 4.6058665E-03 8.7896347E-02 at 150iterations 2.6777338E-03 5.2421570E-02 at 160iterations 1.5754024E-03 3.0557632E-02 at 170iterations 9.4892381E-04 1.9307137E-02 at 180iterations finished qdiffx linear iterations at : 17:04:25 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 9.4892381E-04 1.9307137E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 17:04:25 13.231u 0.257s 0:14.12 95.4% 0+0k 0+0io 0pf+0w