Sat Oct 8 23:52:20 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 23:52:21 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 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: 0.6521221 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): 1.9000053E-02 53.08800 ymin,ymax (A): 8.092000 49.75800 zmin,zma (A): -6.349000 48.24200 x,y,z range (A): 53.06900 41.66600 54.59100 scale (grids/A): 0.6521221 object centre (A): 26.55350 28.92500 20.94650 number of atom coordinates read : 2402 total number of charged atoms : 2263 net assigned charge : 12.42002 assigned positive charge : 354.2583 centred at (gu) : 90.08102 90.83726 89.04554 assigned negative charge : -341.8390 centred at (gu) : 90.08668 90.78516 89.04183 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 48882 no. pairs analyzed = 48882 no. exposed pairs = 3113 no. arc points = 22141 no. surface atoms = 1043 nbur = 1359 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3659 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2800000 number of dielectric boundary points 3562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2220 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0155949E-08 2.1343048E-08 midg,1,midg; midg,igrid,midg 1.5194203E-08 3.8880479E-08 1,midg,midg; igrid,midg,midg 2.5729150E-08 2.4955634E-08 gauss-seidel spectral radius is 0.9878019 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 23:52:21 rms-change max change #iterations 0.1526522 22.21464 at 10iterations 1.6175788E-02 2.425781 at 20iterations 1.7293221E-03 0.2718210 at 30iterations 2.8442053E-04 5.0579071E-02 at 40iterations 8.4858992E-05 1.6431808E-02 at 50iterations finished qdiffx linear iterations at : 23:52:24 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.4858992E-05 1.6431808E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 23:52:24 3.415u 0.239s 0:03.92 92.8% 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 8 2011 at 23:52:24 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.956366 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): 1.9000053E-02 53.08800 ymin,ymax (A): 8.092000 49.75800 zmin,zma (A): -6.349000 48.24200 x,y,z range (A): 53.06900 41.66600 54.59100 scale (grids/A): 1.956366 object centre (A): 26.55350 28.92500 20.94650 number of atom coordinates read : 2402 total number of charged atoms : 2263 net assigned charge : 12.42002 assigned positive charge : 354.2583 centred at (gu) : 90.24270 92.51127 87.13622 assigned negative charge : -341.8390 centred at (gu) : 90.26008 92.35530 87.12538 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22141 grid for indexing accessible points = 1.400000 m= 26896 mr = 49722 m= 4708 mr = 19618 m= 323 mr = 2876 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1979 time to turn everything in is 0.5500000 number of dielectric boundary points 33239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17890 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) : 0.6521221 object centre at (A) : 26.55350 28.92500 20.94650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0368386E-02 5.4689113E-02 midg,1,midg; midg,igrid,midg 3.4314003E-03 3.4016639E-02 1,midg,midg; igrid,midg,midg 5.4864548E-02 4.8973814E-02 gauss-seidel spectral radius is 0.9986916 estimated iterations to convergence 219 setup time was (sec) 0.8500000 now iterating at: 23:52:26 rms-change max change #iterations 4.215053 181.2724 at 10iterations 2.011745 72.15369 at 20iterations 0.9536586 31.86259 at 30iterations 0.4543660 14.94244 at 40iterations 0.2158159 7.641783 at 50iterations 0.1023682 3.354791 at 60iterations 4.8605852E-02 1.437723 at 70iterations 2.3273373E-02 0.7214184 at 80iterations 1.1099319E-02 0.3580180 at 90iterations 5.3196466E-03 0.1650934 at 100iterations 2.5860716E-03 8.1737518E-02 at 110iterations 1.2844824E-03 4.1862488E-02 at 120iterations finished qdiffx linear iterations at : 23:52:32 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.2844824E-03 4.1862488E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 23:52:33 7.647u 0.227s 0:08.21 95.7% 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 8 2011 at 23:52:33 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2402 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 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: 2.934550 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): 1.9000053E-02 53.08800 ymin,ymax (A): 8.092000 49.75800 zmin,zma (A): -6.349000 48.24200 x,y,z range (A): 53.06900 41.66600 54.59100 scale (grids/A): 2.934550 object centre (A): 26.55350 28.92500 20.94650 number of atom coordinates read : 2402 total number of charged atoms : 2263 net assigned charge : 12.42002 assigned positive charge : 354.2583 centred at (gu) : 90.36407 93.76665 85.70435 assigned negative charge : -341.8390 centred at (gu) : 90.39001 93.53309 85.68809 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 169976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22141 grid for indexing accessible points = 1.400000 m= 85642 mr = 120616 m= 32528 mr = 69350 m= 8685 mr = 25976 m= 1403 mr = 6505 m= 113 mr = 924 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 6782 time to turn everything in is 1.350000 number of dielectric boundary points 74925 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 18102 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) : 1.956366 object centre at (A) : 26.55350 28.92500 20.94650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4687067 0.7711800 midg,1,midg; midg,igrid,midg 8.8018775E-03 0.3182573 1,midg,midg; igrid,midg,midg 0.5554029 0.4600558 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.680000 now iterating at: 23:52:35 rms-change max change #iterations 9.996301 419.3248 at 10iterations 5.953510 161.4172 at 20iterations 3.516717 68.52951 at 30iterations 2.063233 45.42050 at 40iterations 1.212147 26.29627 at 50iterations 0.7073039 13.26086 at 60iterations 0.4136517 7.387751 at 70iterations 0.2409308 4.522875 at 80iterations 0.1400572 2.499329 at 90iterations 8.1383169E-02 1.564366 at 100iterations 4.7452088E-02 0.9688778 at 110iterations 2.7530260E-02 0.4813056 at 120iterations 1.6014354E-02 0.3176651 at 130iterations 9.3113557E-03 0.1772156 at 140iterations 5.4122582E-03 9.8125458E-02 at 150iterations 3.1619356E-03 5.7960510E-02 at 160iterations 1.8535450E-03 3.6476135E-02 at 170iterations 1.1035535E-03 2.2930145E-02 at 180iterations finished qdiffx linear iterations at : 23:52:45 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 1.1035535E-03 2.2930145E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.65000 DelPhi exited at 23:52:46 12.652u 0.263s 0:13.23 97.5% 0+0k 0+0io 0pf+0w