Sat Oct 8 14:18:38 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 14:18:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3044 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6350112 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): -14.47000 35.27000 ymin,ymax (A): -11.67700 44.38500 zmin,zma (A): -39.98600 12.68500 x,y,z range (A): 49.74000 56.06200 52.67100 scale (grids/A): 0.6350112 object centre (A): 10.40000 16.35400 -13.65050 number of atom coordinates read : 3044 total number of charged atoms : 2897 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8246 centred at (gu) : 91.77724 91.99959 91.15379 assigned negative charge : -455.8253 centred at (gu) : 91.82844 91.91597 91.22897 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8100 nv = 96 ne = 84 npr = 63818 no. pairs analyzed = 63818 no. exposed pairs = 3486 no. arc points = 24214 no. surface atoms = 1184 nbur = 1860 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 4730 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2340 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8767672E-09 -1.1549249E-08 midg,1,midg; midg,igrid,midg -6.4516379E-09 1.5329208E-08 1,midg,midg; igrid,midg,midg 4.1093009E-09 -9.0085770E-09 gauss-seidel spectral radius is 0.9871849 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 14:18:39 rms-change max change #iterations 0.1586442 19.94058 at 10iterations 1.5849004E-02 2.155220 at 20iterations 1.6387635E-03 0.1941109 at 30iterations 1.9519137E-04 2.5001526E-02 at 40iterations 3.0379417E-05 4.5242310E-03 at 50iterations finished qdiffx linear iterations at : 14:18:42 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 3.0379417E-05 4.5242310E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 14:18:43 4.611u 0.367s 0:05.29 93.9% 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 8 2011 at 14:18:43 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3044 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.905034 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): -14.47000 35.27000 ymin,ymax (A): -11.67700 44.38500 zmin,zma (A): -39.98600 12.68500 x,y,z range (A): 49.74000 56.06200 52.67100 scale (grids/A): 1.905034 object centre (A): 10.40000 16.35400 -13.65050 number of atom coordinates read : 3044 total number of charged atoms : 2897 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8246 centred at (gu) : 95.33145 95.99764 93.46094 assigned negative charge : -455.8253 centred at (gu) : 95.48506 95.74767 93.68664 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24214 grid for indexing accessible points = 1.400000 m= 32028 mr = 63744 m= 4663 mr = 24070 m= 227 mr = 2869 m= 8 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 220 time to turn everything in is 0.7000000 number of dielectric boundary points 34516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22807 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) : 0.6350112 object centre at (A) : 10.40000 16.35400 -13.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7807500E-02 8.5616922E-03 midg,1,midg; midg,igrid,midg -2.4065899E-02 5.3735577E-02 1,midg,midg; igrid,midg,midg 8.4555373E-03 -1.8446572E-02 gauss-seidel spectral radius is 0.9986677 estimated iterations to convergence 217 setup time was (sec) 1.020000 now iterating at: 14:18:45 rms-change max change #iterations 4.702570 197.7775 at 10iterations 2.227601 69.90901 at 20iterations 1.055561 30.26556 at 30iterations 0.4998700 16.25265 at 40iterations 0.2373277 6.583251 at 50iterations 0.1123032 3.461315 at 60iterations 5.3185754E-02 1.564293 at 70iterations 2.5142847E-02 0.7714415 at 80iterations 1.1930442E-02 0.3242998 at 90iterations 5.6586131E-03 0.1562576 at 100iterations 2.6864440E-03 7.6613426E-02 at 110iterations 1.2787769E-03 3.5083771E-02 at 120iterations finished qdiffx linear iterations at : 14:18:54 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 1.2787769E-03 3.5083771E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 14:18:55 11.138u 0.439s 0:11.92 96.9% 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 8 2011 at 14:18:55 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3044 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.857550 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): -14.47000 35.27000 ymin,ymax (A): -11.67700 44.38500 zmin,zma (A): -39.98600 12.68500 x,y,z range (A): 49.74000 56.06200 52.67100 scale (grids/A): 2.857550 object centre (A): 10.40000 16.35400 -13.65050 number of atom coordinates read : 3044 total number of charged atoms : 2897 net assigned charge : 7.1674585E-06 assigned positive charge : 455.8246 centred at (gu) : 97.99693 98.99620 95.19131 assigned negative charge : -455.8253 centred at (gu) : 98.22742 98.62151 95.52987 start vw surface at 0.1400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 204774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24214 grid for indexing accessible points = 1.400000 m= 105261 mr = 154421 m= 36914 mr = 87473 m= 8265 mr = 29865 m= 1101 mr = 6096 m= 61 mr = 686 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 874 time to turn everything in is 1.870000 number of dielectric boundary points 77814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 23175 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) : 1.905034 object centre at (A) : 10.40000 16.35400 -13.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1552855 0.2860767 midg,1,midg; midg,igrid,midg -0.1769677 0.7169734 1,midg,midg; igrid,midg,midg 0.1144883 -0.1299713 gauss-seidel spectral radius is 0.9992714 estimated iterations to convergence 292 setup time was (sec) 2.200000 now iterating at: 14:18:58 rms-change max change #iterations 10.90407 415.8677 at 10iterations 6.392411 123.3165 at 20iterations 3.724257 73.78716 at 30iterations 2.170322 38.77235 at 40iterations 1.260671 27.46032 at 50iterations 0.7301970 14.88290 at 60iterations 0.4234424 7.076286 at 70iterations 0.2449635 3.909892 at 80iterations 0.1418096 2.250101 at 90iterations 8.2079723E-02 1.336632 at 100iterations 4.7493249E-02 0.7815962 at 110iterations 2.7460545E-02 0.4661551 at 120iterations 1.5844010E-02 0.2617569 at 130iterations 9.1936896E-03 0.1436806 at 140iterations 5.3137648E-03 0.1057091 at 150iterations 3.0805387E-03 4.9098969E-02 at 160iterations 1.7860126E-03 3.4846306E-02 at 170iterations 1.0411998E-03 1.7395973E-02 at 180iterations finished qdiffx linear iterations at : 14:19:14 total time elapsed so far: 18.92000 # loops : 180 mean,max change (kT/e) : 1.0411998E-03 1.7395973E-02 energy calculations done at 18.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.07000 DelPhi exited at 14:19:15 19.079u 0.490s 0:19.87 98.4% 0+0k 0+0io 0pf+0w