Sat Oct 15 14:39:46 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 14:39:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5630862 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): -13.87700 49.34600 ymin,ymax (A): -26.46200 17.55600 zmin,zma (A): -41.92800 5.544000 x,y,z range (A): 63.22300 44.01800 47.47200 scale (grids/A): 0.5630862 object centre (A): 17.73450 -4.453000 -18.19200 number of atom coordinates read : 2753 total number of charged atoms : 2614 net assigned charge : -0.9859737 assigned positive charge : 416.6113 centred at (gu) : 89.83513 89.67046 89.14950 assigned negative charge : -417.5984 centred at (gu) : 89.86245 89.53223 88.99628 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5755 nv = 96 ne = 84 npr = 54687 no. pairs analyzed = 54687 no. exposed pairs = 3589 no. arc points = 25655 no. surface atoms = 1205 nbur = 1548 mkacc time = 8.9999996E-02 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= 223 mr = 2923 m= 0 mr = 5 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3050 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2647 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7416 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3461326E-09 1.3420954E-09 midg,1,midg; midg,igrid,midg -1.8684483E-09 1.3691230E-09 1,midg,midg; igrid,midg,midg 2.3285016E-10 -3.9448436E-10 gauss-seidel spectral radius is 0.9837152 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 14:39:47 rms-change max change #iterations 8.3986863E-02 13.39625 at 10iterations 6.0049971E-03 1.097408 at 20iterations 4.2870146E-04 7.4793100E-02 at 30iterations 3.1463052E-05 5.5332184E-03 at 40iterations 2.2816700E-06 4.1580200E-04 at 50iterations finished qdiffx linear iterations at : 14:39:50 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.2816700E-06 4.1580200E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 14:39:51 3.450u 0.197s 0:04.56 79.8% 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 14:39:51 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.689259 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): -13.87700 49.34600 ymin,ymax (A): -26.46200 17.55600 zmin,zma (A): -41.92800 5.544000 x,y,z range (A): 63.22300 44.01800 47.47200 scale (grids/A): 1.689259 object centre (A): 17.73450 -4.453000 -18.19200 number of atom coordinates read : 2753 total number of charged atoms : 2614 net assigned charge : -0.9859737 assigned positive charge : 416.6113 centred at (gu) : 89.50462 89.01060 87.44761 assigned negative charge : -417.5984 centred at (gu) : 89.58701 88.59641 86.98866 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63289 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25655 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18768 mr = 42066 m= 1867 mr = 12654 m= 46 mr = 915 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 1053 time to turn everything in is 0.3100000 number of dielectric boundary points 28328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 20135 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) : 0.5630862 object centre at (A) : 17.73450 -4.453000 -18.19200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5126088E-02 5.5909855E-03 midg,1,midg; midg,igrid,midg -4.6798559E-03 2.7994416E-03 1,midg,midg; igrid,midg,midg 3.6009664E-03 4.4211969E-03 gauss-seidel spectral radius is 0.9982849 estimated iterations to convergence 192 setup time was (sec) 0.5300000 now iterating at: 14:39:52 rms-change max change #iterations 3.472956 163.3199 at 10iterations 1.476767 59.07738 at 20iterations 0.6312101 21.31029 at 30iterations 0.2685171 10.19919 at 40iterations 0.1148713 4.039070 at 50iterations 4.9014393E-02 1.817339 at 60iterations 2.0872414E-02 0.7265924 at 70iterations 8.9217750E-03 0.3244133 at 80iterations 3.8088383E-03 0.1407957 at 90iterations 1.6290832E-03 5.9419632E-02 at 100iterations 6.9522782E-04 2.7007103E-02 at 110iterations 2.9778655E-04 1.0857582E-02 at 120iterations finished qdiffx linear iterations at : 14:40:03 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 2.9778655E-04 1.0857582E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:40:04 7.779u 0.222s 0:13.03 61.3% 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 14:40:04 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.533888 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): -13.87700 49.34600 ymin,ymax (A): -26.46200 17.55600 zmin,zma (A): -41.92800 5.544000 x,y,z range (A): 63.22300 44.01800 47.47200 scale (grids/A): 2.533888 object centre (A): 17.73450 -4.453000 -18.19200 number of atom coordinates read : 2753 total number of charged atoms : 2614 net assigned charge : -0.9859737 assigned positive charge : 416.6113 centred at (gu) : 89.25690 88.51576 86.17124 assigned negative charge : -417.5984 centred at (gu) : 89.38035 87.89458 85.48290 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 147069 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25655 grid for indexing accessible points = 1.400000 m= 65760 mr = 103290 m= 18248 mr = 51340 m= 2754 mr = 13584 m= 180 mr = 1784 m= 6 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3582 time to turn everything in is 0.7500000 number of dielectric boundary points 63933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 20896 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) : 1.689259 object centre at (A) : 17.73450 -4.453000 -18.19200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1822909 9.0825662E-02 midg,1,midg; midg,igrid,midg -4.9463559E-02 2.4377652E-02 1,midg,midg; igrid,midg,midg 8.0865920E-02 0.4283896 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 0.9800000 now iterating at: 14:40:05 rms-change max change #iterations 8.878715 391.8188 at 10iterations 5.003591 129.4356 at 20iterations 2.813507 69.35176 at 30iterations 1.576531 36.52900 at 40iterations 0.8794765 20.43914 at 50iterations 0.4922311 9.749603 at 60iterations 0.2738045 5.424759 at 70iterations 0.1523402 3.080619 at 80iterations 8.4637195E-02 2.023039 at 90iterations 4.6870399E-02 1.059830 at 100iterations 2.6038060E-02 0.5742607 at 110iterations 1.4456970E-02 0.2991686 at 120iterations 8.0280527E-03 0.1557941 at 130iterations 4.4522374E-03 8.9753389E-02 at 140iterations 2.4630779E-03 5.0799370E-02 at 150iterations 1.3716347E-03 2.6249409E-02 at 160iterations 7.6030754E-04 1.4963150E-02 at 170iterations 4.2155333E-04 9.5221996E-03 at 180iterations finished qdiffx linear iterations at : 14:40:26 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 4.2155333E-04 9.5221996E-03 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 14:40:27 12.336u 0.231s 0:23.20 54.1% 0+0k 0+0io 0pf+0w