Sat Oct 15 13:15:26 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 13:15:26 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 !!! WARNING: HIR 108 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5110170 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): -35.78200 12.72100 ymin,ymax (A): 31.21100 85.33700 zmin,zma (A): -16.74900 52.91600 x,y,z range (A): 48.50300 54.12600 69.66500 scale (grids/A): 0.5110170 object centre (A): -11.53050 58.27400 18.08350 number of atom coordinates read : 3219 total number of charged atoms : 3077 net assigned charge : 3.514008 assigned positive charge : 503.5135 centred at (gu) : 90.07087 88.89108 90.26913 assigned negative charge : -500.0006 centred at (gu) : 90.13847 88.78957 90.14609 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5400 nv = 96 ne = 84 npr = 62577 no. pairs analyzed = 62577 no. exposed pairs = 4371 no. arc points = 30352 no. surface atoms = 1469 nbur = 1750 mkacc time = 0.2000000 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 = 1.652000 m= 176 mr = 2536 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2999 ## 454 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 7180 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6569184E-10 2.9681593E-10 midg,1,midg; midg,igrid,midg -1.8594791E-10 1.7759290E-10 1,midg,midg; igrid,midg,midg 1.7326769E-10 -7.4629289E-11 gauss-seidel spectral radius is 0.9803118 estimated iterations to convergence 59 setup time was (sec) 0.8000000 now iterating at: 13:15:28 rms-change max change #iterations 5.6052648E-02 11.37551 at 10iterations 3.1214168E-03 0.5554619 at 20iterations 2.0958355E-04 3.4989357E-02 at 30iterations 2.3660878E-05 3.1814575E-03 at 40iterations 3.8459102E-06 3.9100647E-04 at 50iterations finished qdiffx linear iterations at : 13:15:32 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 3.8459102E-06 3.9100647E-04 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.880000 DelPhi exited at 13:15:34 5.886u 0.477s 0:07.35 86.3% 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 Sat Oct 15 2011 at 13:15:34 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 !!! WARNING: HIR 108 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.533051 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): -35.78200 12.72100 ymin,ymax (A): 31.21100 85.33700 zmin,zma (A): -16.74900 52.91600 x,y,z range (A): 48.50300 54.12600 69.66500 scale (grids/A): 1.533051 object centre (A): -11.53050 58.27400 18.08350 number of atom coordinates read : 3219 total number of charged atoms : 3077 net assigned charge : 3.514008 assigned positive charge : 503.5135 centred at (gu) : 90.21188 86.67258 90.80660 assigned negative charge : -500.0006 centred at (gu) : 90.41486 86.36810 90.43798 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 60921 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30352 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 15575 mr = 39336 m= 1145 mr = 9758 m= 24 mr = 410 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.6300000 number of dielectric boundary points 28161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23094 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) : 0.5110170 object centre at (A) : -11.53050 58.27400 18.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0551922E-02 1.1502437E-02 midg,1,midg; midg,igrid,midg -2.9775822E-03 1.8037821E-04 1,midg,midg; igrid,midg,midg 3.1293510E-03 2.5352759E-03 gauss-seidel spectral radius is 0.9979600 estimated iterations to convergence 176 setup time was (sec) 0.9700000 now iterating at: 13:15:35 rms-change max change #iterations 3.079054 164.3875 at 10iterations 1.216361 52.27444 at 20iterations 0.4801106 17.34700 at 30iterations 0.1891441 7.175056 at 40iterations 7.5056262E-02 3.413488 at 50iterations 2.9675653E-02 1.196460 at 60iterations 1.1745414E-02 0.4826460 at 70iterations 4.6408009E-03 0.1828136 at 80iterations 1.8397627E-03 7.8844070E-02 at 90iterations 7.3120429E-04 2.7872443E-02 at 100iterations 2.9061409E-04 1.1492729E-02 at 110iterations 1.1522786E-04 4.2819977E-03 at 120iterations finished qdiffx linear iterations at : 13:15:46 total time elapsed so far: 11.08000 # loops : 120 mean,max change (kT/e) : 1.1522786E-04 4.2819977E-03 energy calculations done at 11.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 13:15:47 11.312u 0.522s 0:13.01 90.9% 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 13:15:47 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3219 !!! WARNING: HIR 108 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.299577 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): -35.78200 12.72100 ymin,ymax (A): 31.21100 85.33700 zmin,zma (A): -16.74900 52.91600 x,y,z range (A): 48.50300 54.12600 69.66500 scale (grids/A): 2.299577 object centre (A): -11.53050 58.27400 18.08350 number of atom coordinates read : 3219 total number of charged atoms : 3077 net assigned charge : 3.514008 assigned positive charge : 503.5135 centred at (gu) : 90.31770 85.00865 91.20964 assigned negative charge : -500.0006 centred at (gu) : 90.62219 84.55204 90.65685 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 142172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30352 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 58083 mr = 97739 m= 12534 mr = 43770 m= 1558 mr = 8554 m= 84 mr = 855 m= 0 mr = 20 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1024 time to turn everything in is 1.500000 number of dielectric boundary points 63493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 54 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 24536 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) : 1.533051 object centre at (A) : -11.53050 58.27400 18.08350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1245355 0.1519505 midg,1,midg; midg,igrid,midg -1.3914282E-02 -1.1707228E-02 1,midg,midg; igrid,midg,midg 4.2079076E-02 4.4805475E-02 gauss-seidel spectral radius is 0.9990830 estimated iterations to convergence 261 setup time was (sec) 1.880000 now iterating at: 13:15:50 rms-change max change #iterations 8.514831 316.1263 at 10iterations 4.753689 134.7405 at 20iterations 2.615849 67.77578 at 30iterations 1.439748 37.99075 at 40iterations 0.7857842 18.49974 at 50iterations 0.4281906 9.696118 at 60iterations 0.2330317 5.692927 at 70iterations 0.1262097 2.961191 at 80iterations 6.8298750E-02 1.699221 at 90iterations 3.7046641E-02 0.7940369 at 100iterations 1.9980233E-02 0.4386978 at 110iterations 1.0817517E-02 0.2248383 at 120iterations 5.8136117E-03 0.1287622 at 130iterations 3.1413524E-03 6.4951226E-02 at 140iterations 1.6929585E-03 3.6429405E-02 at 150iterations 9.1334694E-04 2.0374417E-02 at 160iterations 4.9284688E-04 1.0651588E-02 at 170iterations 2.6552568E-04 6.5460205E-03 at 180iterations finished qdiffx linear iterations at : 13:16:12 total time elapsed so far: 18.77000 # loops : 180 mean,max change (kT/e) : 2.6552568E-04 6.5460205E-03 energy calculations done at 18.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.22000 DelPhi exited at 13:16:13 19.229u 0.534s 0:26.01 75.9% 0+0k 0+0io 0pf+0w