Sat Oct 8 13:47:05 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 8 2011 at 13:47:05 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 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: 0.6316648 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): -11.39000 43.34700 ymin,ymax (A): 10.92000 55.41700 zmin,zma (A): 37.88300 94.24200 x,y,z range (A): 54.73700 44.49700 56.35900 scale (grids/A): 0.6316648 object centre (A): 15.97850 33.16850 66.06250 number of atom coordinates read : 2945 total number of charged atoms : 2798 net assigned charge : -2.985993 assigned positive charge : 441.0557 centred at (gu) : 89.06544 89.39122 90.96935 assigned negative charge : -444.0424 centred at (gu) : 89.02126 89.29978 90.92923 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7884 nv = 96 ne = 84 npr = 60997 no. pairs analyzed = 60997 no. exposed pairs = 3430 no. arc points = 23350 no. surface atoms = 1168 nbur = 1777 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 429 mr = 4679 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1687588E-09 1.1617870E-09 midg,1,midg; midg,igrid,midg -1.4969055E-08 5.4449396E-09 1,midg,midg; igrid,midg,midg -9.8334274E-09 1.0474187E-09 gauss-seidel spectral radius is 0.9870431 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 13:47:06 rms-change max change #iterations 0.1511773 21.89859 at 10iterations 1.5093150E-02 2.406781 at 20iterations 1.6485922E-03 0.2528419 at 30iterations 2.5736971E-04 3.9710999E-02 at 40iterations 5.8542635E-05 9.8361969E-03 at 50iterations finished qdiffx linear iterations at : 13:47:08 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 5.8542635E-05 9.8361969E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:47:09 3.312u 0.158s 0:03.78 91.5% 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 13:47:09 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.894994 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): -11.39000 43.34700 ymin,ymax (A): 10.92000 55.41700 zmin,zma (A): 37.88300 94.24200 x,y,z range (A): 54.73700 44.49700 56.35900 scale (grids/A): 1.894994 object centre (A): 15.97850 33.16850 66.06250 number of atom coordinates read : 2945 total number of charged atoms : 2798 net assigned charge : -2.985993 assigned positive charge : 441.0557 centred at (gu) : 87.19579 88.17300 92.90747 assigned negative charge : -444.0424 centred at (gu) : 87.06355 87.89902 92.78748 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 86395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23350 grid for indexing accessible points = 1.400000 m= 32291 mr = 62929 m= 4977 mr = 24672 m= 277 mr = 3129 m= 2 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 33119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21960 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) : 0.6316648 object centre at (A) : 15.97850 33.16850 66.06250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7504262E-02 6.8237130E-03 midg,1,midg; midg,igrid,midg -5.4747458E-03 1.1057111E-02 1,midg,midg; igrid,midg,midg -5.8720253E-02 -2.4688547E-03 gauss-seidel spectral radius is 0.9986514 estimated iterations to convergence 216 setup time was (sec) 0.9700000 now iterating at: 13:47:10 rms-change max change #iterations 4.573452 175.5628 at 10iterations 2.161685 70.33890 at 20iterations 1.019633 31.14802 at 30iterations 0.4798844 13.79582 at 40iterations 0.2258540 6.539925 at 50iterations 0.1067778 3.125427 at 60iterations 5.0161414E-02 1.448201 at 70iterations 2.3780106E-02 0.7544832 at 80iterations 1.1229586E-02 0.3335830 at 90iterations 5.3158142E-03 0.1740875 at 100iterations 2.5131081E-03 7.3924065E-02 at 110iterations 1.2003395E-03 3.5301208E-02 at 120iterations finished qdiffx linear iterations at : 13:47:17 total time elapsed so far: 8.560000 # loops : 120 mean,max change (kT/e) : 1.2003395E-03 3.5301208E-02 energy calculations done at 8.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 13:47:18 8.742u 0.261s 0:09.35 96.2% 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 13:47:18 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2945 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.842492 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): -11.39000 43.34700 ymin,ymax (A): 10.92000 55.41700 zmin,zma (A): 37.88300 94.24200 x,y,z range (A): 54.73700 44.49700 56.35900 scale (grids/A): 2.842492 object centre (A): 15.97850 33.16850 66.06250 number of atom coordinates read : 2945 total number of charged atoms : 2798 net assigned charge : -2.985993 assigned positive charge : 441.0557 centred at (gu) : 85.79362 87.25945 94.36089 assigned negative charge : -444.0424 centred at (gu) : 85.59536 86.84864 94.18113 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 199893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23350 grid for indexing accessible points = 1.400000 m= 105538 mr = 151691 m= 38211 mr = 88526 m= 8777 mr = 31354 m= 1192 mr = 6578 m= 51 mr = 782 m= 0 mr = 13 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 74718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 22381 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) : 1.894994 object centre at (A) : 15.97850 33.16850 66.06250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8377315E-02 0.1609399 midg,1,midg; midg,igrid,midg -3.3908978E-02 0.1356159 1,midg,midg; igrid,midg,midg -0.8172467 0.1734684 gauss-seidel spectral radius is 0.9992648 estimated iterations to convergence 291 setup time was (sec) 1.910000 now iterating at: 13:47:20 rms-change max change #iterations 10.67121 296.6115 at 10iterations 6.277849 157.7701 at 20iterations 3.654212 71.41263 at 30iterations 2.128904 41.44323 at 40iterations 1.234076 24.06031 at 50iterations 0.7142075 13.99477 at 60iterations 0.4143596 8.345488 at 70iterations 0.2393869 4.381294 at 80iterations 0.1381255 2.284884 at 90iterations 7.9822540E-02 1.289277 at 100iterations 4.6064723E-02 0.9535286 at 110iterations 2.6608175E-02 0.4372520 at 120iterations 1.5344886E-02 0.2458496 at 130iterations 8.8866940E-03 0.1517944 at 140iterations 5.1412364E-03 8.0690145E-02 at 150iterations 2.9864991E-03 5.2078247E-02 at 160iterations 1.7456288E-03 3.1971693E-02 at 170iterations 1.0285955E-03 1.7332077E-02 at 180iterations finished qdiffx linear iterations at : 13:47:35 total time elapsed so far: 17.00000 # loops : 180 mean,max change (kT/e) : 1.0285955E-03 1.7332077E-02 energy calculations done at 17.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.18000 DelPhi exited at 13:47:36 17.179u 0.318s 0:17.81 98.1% 0+0k 0+0io 0pf+0w