Sat Oct 15 15:14:51 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 15:14:51 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: HIR 68 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6464500 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): -12.37700 36.90500 ymin,ymax (A): -27.01700 21.53700 zmin,zma (A): -9.661000 45.40900 x,y,z range (A): 49.28200 48.55400 55.07000 scale (grids/A): 0.6464500 object centre (A): 12.26400 -2.740001 17.87400 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 6.176026 assigned positive charge : 415.3640 centred at (gu) : 90.37213 90.43886 91.65736 assigned negative charge : -409.1884 centred at (gu) : 90.14029 90.25970 91.70158 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7529 nv = 96 ne = 84 npr = 56087 no. pairs analyzed = 56087 no. exposed pairs = 3195 no. arc points = 22258 no. surface atoms = 1075 nbur = 1651 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 4336 m= 0 mr = 45 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3900000 number of dielectric boundary points 3543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2240 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9101 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2147598E-08 5.7336740E-09 midg,1,midg; midg,igrid,midg -1.4472000E-08 3.9899561E-08 1,midg,midg; igrid,midg,midg -2.2106962E-08 4.7306166E-08 gauss-seidel spectral radius is 0.9876056 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 15:14:52 rms-change max change #iterations 0.1571539 22.03649 at 10iterations 1.6187653E-02 2.425485 at 20iterations 1.6575006E-03 0.2197914 at 30iterations 1.6857852E-04 2.1327972E-02 at 40iterations 1.8416369E-05 2.6092529E-03 at 50iterations finished qdiffx linear iterations at : 15:14:55 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.8416369E-05 2.6092529E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 15:14:55 4.033u 0.167s 0:04.51 92.9% 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 15 2011 at 15:14:55 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: HIR 68 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.939350 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): -12.37700 36.90500 ymin,ymax (A): -27.01700 21.53700 zmin,zma (A): -9.661000 45.40900 x,y,z range (A): 49.28200 48.55400 55.07000 scale (grids/A): 1.939350 object centre (A): 12.26400 -2.740001 17.87400 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 6.176026 assigned positive charge : 415.3640 centred at (gu) : 91.11581 91.31609 94.97166 assigned negative charge : -409.1884 centred at (gu) : 90.42061 90.77900 95.10462 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 81112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22258 grid for indexing accessible points = 1.400000 m= 30180 mr = 57801 m= 4618 mr = 22706 m= 263 mr = 2871 m= 6 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1192 time to turn everything in is 0.7100000 number of dielectric boundary points 32691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20297 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) : 0.6464500 object centre at (A) : 12.26400 -2.740001 17.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4614323E-03 1.7765956E-02 midg,1,midg; midg,igrid,midg -1.1637854E-02 3.0397508E-02 1,midg,midg; igrid,midg,midg -5.7097976E-03 5.9229758E-02 gauss-seidel spectral radius is 0.9986874 estimated iterations to convergence 219 setup time was (sec) 1.060000 now iterating at: 15:14:57 rms-change max change #iterations 4.560024 188.8362 at 10iterations 2.176677 70.22590 at 20iterations 1.035418 30.85517 at 30iterations 0.4923734 15.45219 at 40iterations 0.2346648 7.096389 at 50iterations 0.1116735 3.143341 at 60iterations 5.3276848E-02 1.825464 at 70iterations 2.5358103E-02 0.7464333 at 80iterations 1.2070108E-02 0.3541851 at 90iterations 5.7575973E-03 0.1899529 at 100iterations 2.7512300E-03 8.1842422E-02 at 110iterations 1.3128489E-03 4.0199280E-02 at 120iterations finished qdiffx linear iterations at : 15:15:04 total time elapsed so far: 8.720000 # loops : 120 mean,max change (kT/e) : 1.3128489E-03 4.0199280E-02 energy calculations done at 8.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.950000 DelPhi exited at 15:15:05 8.950u 0.198s 0:09.65 94.7% 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 15:15:05 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 !!! WARNING: HIR 68 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.909025 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): -12.37700 36.90500 ymin,ymax (A): -27.01700 21.53700 zmin,zma (A): -9.661000 45.40900 x,y,z range (A): 49.28200 48.55400 55.07000 scale (grids/A): 2.909025 object centre (A): 12.26400 -2.740001 17.87400 number of atom coordinates read : 2726 total number of charged atoms : 2574 net assigned charge : 6.176026 assigned positive charge : 415.3640 centred at (gu) : 91.67367 91.97402 97.45744 assigned negative charge : -409.1884 centred at (gu) : 90.63082 91.16827 97.65684 start vw surface at 0.1900000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 187384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22258 grid for indexing accessible points = 1.400000 m= 97948 mr = 139322 m= 35441 mr = 81480 m= 8266 mr = 28754 m= 1201 mr = 6211 m= 77 mr = 806 m= 3 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 3730 time to turn everything in is 1.860000 number of dielectric boundary points 73712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 20586 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) : 1.939350 object centre at (A) : 12.26400 -2.740001 17.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1599397 0.3798673 midg,1,midg; midg,igrid,midg -0.1542038 0.3542947 1,midg,midg; igrid,midg,midg -3.2438386E-02 0.4994343 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 2.220000 now iterating at: 15:15:08 rms-change max change #iterations 10.59272 362.5214 at 10iterations 6.220265 148.9511 at 20iterations 3.628645 72.65588 at 30iterations 2.110410 45.38309 at 40iterations 1.228921 23.16705 at 50iterations 0.7125487 13.93704 at 60iterations 0.4126698 6.982937 at 70iterations 0.2387961 4.619921 at 80iterations 0.1385420 2.318912 at 90iterations 8.0136292E-02 1.508862 at 100iterations 4.6256524E-02 0.8352928 at 110iterations 2.6724553E-02 0.4568176 at 120iterations 1.5456225E-02 0.2740879 at 130iterations 8.9256642E-03 0.1568604 at 140iterations 5.1631164E-03 8.8583946E-02 at 150iterations 2.9737486E-03 4.9510956E-02 at 160iterations 1.7192084E-03 3.3340693E-02 at 170iterations 9.9191791E-04 1.7111421E-02 at 180iterations finished qdiffx linear iterations at : 15:15:20 total time elapsed so far: 14.21000 # loops : 180 mean,max change (kT/e) : 9.9191791E-04 1.7111421E-02 energy calculations done at 14.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.43000 DelPhi exited at 15:15:20 14.435u 0.196s 0:14.99 97.5% 0+0k 0+0io 0pf+0w