Sat Oct 8 16:35:24 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+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 Sat Oct 8 2011 at 16:35:24 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4631 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5453765 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): 16.99300 78.78500 ymin,ymax (A): 120.0730 185.3490 zmin,zma (A): -1.955000 59.50300 x,y,z range (A): 61.79200 65.27600 61.45800 scale (grids/A): 0.5453765 object centre (A): 47.88900 152.7110 28.77400 number of atom coordinates read : 4631 total number of charged atoms : 4423 net assigned charge : 3.000041 assigned positive charge : 706.1317 centred at (gu) : 91.61732 89.17010 87.26088 assigned negative charge : -703.1349 centred at (gu) : 91.57954 89.08411 87.27775 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8774 nv = 96 ne = 84 npr = 94045 no. pairs analyzed = 94045 no. exposed pairs = 5467 no. arc points = 38430 no. surface atoms = 1831 nbur = 2800 mkacc time = 0.2100000 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 = 1.568000 m= 393 mr = 4804 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.4400000 number of dielectric boundary points 4345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3771 ## 464 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11544 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8776634E-10 5.3810623E-12 midg,1,midg; midg,igrid,midg -8.7158264E-10 8.4448448E-10 1,midg,midg; igrid,midg,midg -1.3701505E-10 8.3571994E-10 gauss-seidel spectral radius is 0.9827871 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 16:35:25 rms-change max change #iterations 9.2318922E-02 13.03078 at 10iterations 6.6516106E-03 0.8147202 at 20iterations 6.9516676E-04 8.9351654E-02 at 30iterations 1.7048864E-04 2.5156021E-02 at 40iterations 5.1850751E-05 7.7776909E-03 at 50iterations finished qdiffx linear iterations at : 16:35:27 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 5.1850751E-05 7.7776909E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 16:35:28 3.477u 0.185s 0:03.99 91.4% 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 8 2011 at 16:35:28 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4631 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.636130 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): 16.99300 78.78500 ymin,ymax (A): 120.0730 185.3490 zmin,zma (A): -1.955000 59.50300 x,y,z range (A): 61.79200 65.27600 61.45800 scale (grids/A): 1.636130 object centre (A): 47.88900 152.7110 28.77400 number of atom coordinates read : 4631 total number of charged atoms : 4423 net assigned charge : 3.000041 assigned positive charge : 706.1317 centred at (gu) : 94.85081 87.50947 81.78152 assigned negative charge : -703.1349 centred at (gu) : 94.73853 87.25198 81.83306 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 99074 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 30723 mr = 69755 m= 3509 mr = 21512 m= 103 mr = 1935 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1551 time to turn everything in is 0.6900000 number of dielectric boundary points 40200 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 435 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 33836 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) : 0.5453765 object centre at (A) : 47.88900 152.7110 28.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0535621E-03 8.3736395E-03 midg,1,midg; midg,igrid,midg 1.4529441E-02 3.4946300E-02 1,midg,midg; igrid,midg,midg -1.0751638E-02 -1.5327471E-02 gauss-seidel spectral radius is 0.9983457 estimated iterations to convergence 195 setup time was (sec) 0.9900000 now iterating at: 16:35:29 rms-change max change #iterations 4.367765 252.7626 at 10iterations 1.889835 85.83513 at 20iterations 0.8200806 33.49970 at 30iterations 0.3557294 12.11559 at 40iterations 0.1544148 4.712382 at 50iterations 6.7225486E-02 1.930674 at 60iterations 2.9246883E-02 0.9726124 at 70iterations 1.2733181E-02 0.3861935 at 80iterations 5.5504008E-03 0.1651268 at 90iterations 2.4303698E-03 7.3431015E-02 at 100iterations 1.0729567E-03 3.0634880E-02 at 110iterations 4.7984772E-04 1.4210701E-02 at 120iterations finished qdiffx linear iterations at : 16:35:36 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 4.7984772E-04 1.4210701E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 16:35:36 8.013u 0.216s 0:08.55 96.1% 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 Sat Oct 8 2011 at 16:35:36 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4631 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.454195 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): 16.99300 78.78500 ymin,ymax (A): 120.0730 185.3490 zmin,zma (A): -1.955000 59.50300 x,y,z range (A): 61.79200 65.27600 61.45800 scale (grids/A): 2.454195 object centre (A): 47.88900 152.7110 28.77400 number of atom coordinates read : 4631 total number of charged atoms : 4423 net assigned charge : 3.000041 assigned positive charge : 706.1317 centred at (gu) : 97.27596 86.26394 77.67189 assigned negative charge : -703.1349 centred at (gu) : 97.10762 85.87799 77.74954 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 230582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38430 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106835 mr = 170436 m= 31101 mr = 85544 m= 5829 mr = 23699 m= 517 mr = 4123 m= 12 mr = 285 m= 0 mr = 2 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 5050 time to turn everything in is 1.580000 number of dielectric boundary points 90787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 35344 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) : 1.636130 object centre at (A) : 47.88900 152.7110 28.77400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1648173E-02 0.1775841 midg,1,midg; midg,igrid,midg 0.2239813 0.6310596 1,midg,midg; igrid,midg,midg -0.1510153 -0.2219894 gauss-seidel spectral radius is 0.9992161 estimated iterations to convergence 282 setup time was (sec) 1.870000 now iterating at: 16:35:38 rms-change max change #iterations 11.14530 461.1326 at 10iterations 6.432761 204.5101 at 20iterations 3.688116 125.0802 at 30iterations 2.112204 97.15918 at 40iterations 1.206126 38.15019 at 50iterations 0.6875538 15.71221 at 60iterations 0.3905129 9.338256 at 70iterations 0.2210024 4.104413 at 80iterations 0.1254866 2.183092 at 90iterations 7.1408547E-02 1.217178 at 100iterations 4.0313933E-02 0.6867313 at 110iterations 2.2859741E-02 0.3900223 at 120iterations 1.2920190E-02 0.2370510 at 130iterations 7.3237764E-03 0.1229935 at 140iterations 4.1385493E-03 7.5721741E-02 at 150iterations 2.3442449E-03 3.7852287E-02 at 160iterations 1.3257412E-03 2.4456024E-02 at 170iterations 7.4999762E-04 1.2331009E-02 at 180iterations finished qdiffx linear iterations at : 16:35:48 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 7.4999762E-04 1.2331009E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 16:35:49 11.705u 0.166s 0:12.21 97.1% 0+0k 0+0io 0pf+0w