Sat Oct 8 11:36:56 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+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 11:36:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6005803 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): -24.07700 35.19900 ymin,ymax (A): 38.97200 95.17800 zmin,zma (A): 30.82100 89.49600 x,y,z range (A): 59.27600 56.20600 58.67500 scale (grids/A): 0.6005803 object centre (A): 5.561001 67.07500 60.15850 number of atom coordinates read : 4117 total number of charged atoms : 3965 net assigned charge : -2.499945 assigned positive charge : 611.1957 centred at (gu) : 90.27047 89.03114 88.79175 assigned negative charge : -613.6985 centred at (gu) : 90.13170 89.18037 88.92613 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9750 nv = 96 ne = 84 npr = 86968 no. pairs analyzed = 86968 no. exposed pairs = 4515 no. arc points = 30696 no. surface atoms = 1549 nbur = 2568 mkacc time = 0.1500000 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 = 1.456000 m= 462 mr = 5874 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 96 time to turn everything in is 0.2900000 number of dielectric boundary points 4301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3181 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 12450 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5830809E-09 -7.0619772E-09 midg,1,midg; midg,igrid,midg 9.1669055E-09 -8.1760465E-09 1,midg,midg; igrid,midg,midg -8.9935153E-09 7.1507307E-09 gauss-seidel spectral radius is 0.9857669 estimated iterations to convergence 69 setup time was (sec) 0.4900000 now iterating at: 11:36:57 rms-change max change #iterations 0.1401741 18.33878 at 10iterations 1.2424740E-02 1.740000 at 20iterations 1.3142244E-03 0.1566114 at 30iterations 2.7002723E-04 3.3786297E-02 at 40iterations 9.1310758E-05 1.2344360E-02 at 50iterations finished qdiffx linear iterations at : 11:37:00 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 9.1310758E-05 1.2344360E-02 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 11:37:01 3.722u 0.222s 0:04.45 88.5% 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 11:37:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.801741 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): -24.07700 35.19900 ymin,ymax (A): 38.97200 95.17800 zmin,zma (A): 30.82100 89.49600 x,y,z range (A): 59.27600 56.20600 58.67500 scale (grids/A): 1.801741 object centre (A): 5.561001 67.07500 60.15850 number of atom coordinates read : 4117 total number of charged atoms : 3965 net assigned charge : -2.499945 assigned positive charge : 611.1957 centred at (gu) : 90.81041 87.09174 86.37407 assigned negative charge : -613.6985 centred at (gu) : 90.39449 87.54095 86.77792 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 108029 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30696 grid for indexing accessible points = 1.400000 m= 38470 mr = 79713 m= 5517 mr = 29216 m= 245 mr = 3504 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 6123 time to turn everything in is 0.5100000 number of dielectric boundary points 39748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 287 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 30953 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) : 0.6005803 object centre at (A) : 5.561001 67.07500 60.15850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4185154E-02 -3.6314409E-02 midg,1,midg; midg,igrid,midg 3.4694869E-02 -2.5316035E-02 1,midg,midg; igrid,midg,midg -2.0574315E-02 4.5310900E-02 gauss-seidel spectral radius is 0.9986107 estimated iterations to convergence 213 setup time was (sec) 0.7400000 now iterating at: 11:37:02 rms-change max change #iterations 4.936662 171.0758 at 10iterations 2.288545 67.03199 at 20iterations 1.064919 28.57222 at 30iterations 0.4978527 13.11043 at 40iterations 0.2308105 6.598883 at 50iterations 0.1081495 2.860296 at 60iterations 5.0459754E-02 1.416122 at 70iterations 2.3608085E-02 0.6570892 at 80iterations 1.1028824E-02 0.2877426 at 90iterations 5.1459712E-03 0.1333694 at 100iterations 2.4283542E-03 6.3261986E-02 at 110iterations 1.1534351E-03 3.2463074E-02 at 120iterations finished qdiffx linear iterations at : 11:37:09 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 1.1534351E-03 3.2463074E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 11:37:10 8.352u 0.223s 0:09.08 94.3% 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 8 2011 at 11:37:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.702611 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): -24.07700 35.19900 ymin,ymax (A): 38.97200 95.17800 zmin,zma (A): 30.82100 89.49600 x,y,z range (A): 59.27600 56.20600 58.67500 scale (grids/A): 2.702611 object centre (A): 5.561001 67.07500 60.15850 number of atom coordinates read : 4117 total number of charged atoms : 3965 net assigned charge : -2.499945 assigned positive charge : 611.1957 centred at (gu) : 91.21526 85.63731 84.56081 assigned negative charge : -613.6985 centred at (gu) : 90.59169 86.31138 85.16681 start vw surface at 0.1200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 250739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30696 grid for indexing accessible points = 1.400000 m= 128652 mr = 192913 m= 43422 mr = 107557 m= 9754 mr = 35435 m= 1218 mr = 7528 m= 47 mr = 775 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 20462 time to turn everything in is 1.360000 number of dielectric boundary points 89613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.470000 number of grid points assigned charge 31710 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) : 1.801741 object centre at (A) : 5.561001 67.07500 60.15850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8335541 -0.3984112 midg,1,midg; midg,igrid,midg 0.4381303 -0.3504309 1,midg,midg; igrid,midg,midg -0.3142898 0.4343451 gauss-seidel spectral radius is 0.9992744 estimated iterations to convergence 293 setup time was (sec) 1.630000 now iterating at: 11:37:12 rms-change max change #iterations 11.65994 311.4986 at 10iterations 6.839390 117.7570 at 20iterations 3.994054 70.97309 at 30iterations 2.320336 37.35316 at 40iterations 1.349219 27.59866 at 50iterations 0.7837800 13.61411 at 60iterations 0.4536498 7.083149 at 70iterations 0.2627427 4.368167 at 80iterations 0.1523522 2.486614 at 90iterations 8.8253371E-02 1.425261 at 100iterations 5.1060725E-02 0.7951837 at 110iterations 2.9644055E-02 0.4519815 at 120iterations 1.7183248E-02 0.2973213 at 130iterations 9.9883778E-03 0.1552076 at 140iterations 5.8235512E-03 9.9191666E-02 at 150iterations 3.4315293E-03 5.3054810E-02 at 160iterations 2.0457420E-03 3.3329964E-02 at 170iterations 1.2498287E-03 2.1011353E-02 at 180iterations finished qdiffx linear iterations at : 11:37:25 total time elapsed so far: 14.70000 # loops : 180 mean,max change (kT/e) : 1.2498287E-03 2.1011353E-02 energy calculations done at 14.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.83000 DelPhi exited at 11:37:26 14.827u 0.267s 0:15.75 95.7% 0+0k 0+0io 0pf+0w