Sat Oct 8 21:27:22 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 21:27:22 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: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2617 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6433192 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): -28.23200 27.10600 ymin,ymax (A): 16.06600 62.39900 zmin,zma (A): -20.65800 26.92400 x,y,z range (A): 55.33800 46.33300 47.58200 scale (grids/A): 0.6433192 object centre (A): -0.5629997 39.23250 3.133000 number of atom coordinates read : 2617 total number of charged atoms : 2475 net assigned charge : 1.420006 assigned positive charge : 398.3078 centred at (gu) : 90.44616 90.41872 89.01561 assigned negative charge : -396.8883 centred at (gu) : 90.45493 90.39135 89.02671 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7432 nv = 96 ne = 84 npr = 52134 no. pairs analyzed = 52134 no. exposed pairs = 3392 no. arc points = 24246 no. surface atoms = 1125 nbur = 1492 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 4000 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2312 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8724 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5423825E-09 6.6337857E-10 midg,1,midg; midg,igrid,midg -1.2104678E-09 6.3443490E-09 1,midg,midg; igrid,midg,midg 3.0844751E-09 1.1982174E-09 gauss-seidel spectral radius is 0.9874858 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 21:27:23 rms-change max change #iterations 0.1532266 22.24638 at 10iterations 1.5567397E-02 2.160835 at 20iterations 1.5595685E-03 0.1957855 at 30iterations 1.7748328E-04 2.6712179E-02 at 40iterations 3.4215223E-05 4.4784546E-03 at 50iterations finished qdiffx linear iterations at : 21:27:25 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 3.4215223E-05 4.4784546E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 21:27:25 3.109u 0.152s 0:03.52 92.3% 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 21:27:25 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: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2617 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 has a net charge of -0.0940 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: 1.929958 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): -28.23200 27.10600 ymin,ymax (A): 16.06600 62.39900 zmin,zma (A): -20.65800 26.92400 x,y,z range (A): 55.33800 46.33300 47.58200 scale (grids/A): 1.929958 object centre (A): -0.5629997 39.23250 3.133000 number of atom coordinates read : 2617 total number of charged atoms : 2475 net assigned charge : 1.420006 assigned positive charge : 398.3078 centred at (gu) : 91.33776 91.25570 87.04612 assigned negative charge : -396.8883 centred at (gu) : 91.36449 91.17374 87.07957 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 29211 mr = 54654 m= 4933 mr = 20836 m= 324 mr = 2819 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 399 time to turn everything in is 0.5600000 number of dielectric boundary points 35474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19524 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) : 0.6433192 object centre at (A) : -0.5629997 39.23250 3.133000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5630893E-02 -6.4246948E-03 midg,1,midg; midg,igrid,midg -3.5839874E-04 1.3054346E-02 1,midg,midg; igrid,midg,midg 2.0476712E-02 -2.6596442E-02 gauss-seidel spectral radius is 0.9986825 estimated iterations to convergence 218 setup time was (sec) 0.8200000 now iterating at: 21:27:26 rms-change max change #iterations 4.467044 169.7613 at 10iterations 2.121701 74.19868 at 20iterations 1.012578 29.84998 at 30iterations 0.4790125 16.62574 at 40iterations 0.2282285 7.774811 at 50iterations 0.1083260 3.339222 at 60iterations 5.1448222E-02 1.499241 at 70iterations 2.4480920E-02 0.7497463 at 80iterations 1.1580470E-02 0.3594699 at 90iterations 5.5164443E-03 0.1777506 at 100iterations 2.6229611E-03 7.9984665E-02 at 110iterations 1.2450744E-03 4.4506073E-02 at 120iterations finished qdiffx linear iterations at : 21:27:32 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 1.2450744E-03 4.4506073E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 21:27:33 6.926u 0.163s 0:07.36 96.1% 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 21:27:33 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: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2617 !!! WARNING: HIR 88 has a net charge of 0.5140 !!! WARNING: GLM 128 has a net charge of -0.0940 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: 2.894937 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): -28.23200 27.10600 ymin,ymax (A): 16.06600 62.39900 zmin,zma (A): -20.65800 26.92400 x,y,z range (A): 55.33800 46.33300 47.58200 scale (grids/A): 2.894937 object centre (A): -0.5629997 39.23250 3.133000 number of atom coordinates read : 2617 total number of charged atoms : 2475 net assigned charge : 1.420006 assigned positive charge : 398.3078 centred at (gu) : 92.00661 91.88329 85.56905 assigned negative charge : -396.8883 centred at (gu) : 92.04671 91.76052 85.61937 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 183362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24246 grid for indexing accessible points = 1.400000 m= 93569 mr = 132270 m= 34419 mr = 75578 m= 8757 mr = 26627 m= 1386 mr = 6163 m= 78 mr = 799 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1518 time to turn everything in is 1.380000 number of dielectric boundary points 80117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19800 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) : 1.929958 object centre at (A) : -0.5629997 39.23250 3.133000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2005228 -3.5090398E-02 midg,1,midg; midg,igrid,midg -5.9186179E-02 0.1809707 1,midg,midg; igrid,midg,midg 0.1878648 -0.4735731 gauss-seidel spectral radius is 0.9992820 estimated iterations to convergence 294 setup time was (sec) 1.660000 now iterating at: 21:27:35 rms-change max change #iterations 10.56163 416.8883 at 10iterations 6.313821 147.3800 at 20iterations 3.742625 77.50829 at 30iterations 2.206506 45.76676 at 40iterations 1.301652 25.77853 at 50iterations 0.7631497 14.88227 at 60iterations 0.4464902 8.900219 at 70iterations 0.2604916 5.211369 at 80iterations 0.1522309 2.780304 at 90iterations 8.8585652E-02 1.758520 at 100iterations 5.1574819E-02 1.012011 at 110iterations 2.9976595E-02 0.5142241 at 120iterations 1.7404031E-02 0.3135910 at 130iterations 1.0117150E-02 0.1668463 at 140iterations 5.8854497E-03 0.1010448 at 150iterations 3.4201641E-03 5.9364319E-02 at 160iterations 1.9908734E-03 3.7025452E-02 at 170iterations 1.1587508E-03 2.0717621E-02 at 180iterations finished qdiffx linear iterations at : 21:27:44 total time elapsed so far: 11.46000 # loops : 180 mean,max change (kT/e) : 1.1587508E-03 2.0717621E-02 energy calculations done at 11.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 21:27:45 11.645u 0.182s 0:12.09 97.7% 0+0k 0+0io 0pf+0w