Mon Oct 10 21:10:30 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 Mon Oct 10 2011 at 21:10:30 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6802852 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): -23.99200 28.33900 ymin,ymax (A): -11.00300 30.80700 zmin,zma (A): -5.339000 46.72800 x,y,z range (A): 52.33100 41.81000 52.06700 scale (grids/A): 0.6802852 object centre (A): 2.173500 9.902000 20.69450 number of atom coordinates read : 2386 total number of charged atoms : 2253 net assigned charge : 2.000021 assigned positive charge : 347.1422 centred at (gu) : 90.85157 89.12468 88.94240 assigned negative charge : -345.1430 centred at (gu) : 90.81969 89.18517 88.90602 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7707 nv = 96 ne = 84 npr = 48720 no. pairs analyzed = 48720 no. exposed pairs = 3172 no. arc points = 22187 no. surface atoms = 1074 nbur = 1312 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 481 mr = 4120 m= 2 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2800000 number of dielectric boundary points 3980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2022 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8629 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7561757E-09 1.5413821E-08 midg,1,midg; midg,igrid,midg 3.1064364E-08 -7.5946875E-09 1,midg,midg; igrid,midg,midg -5.8716904E-10 2.1081652E-08 gauss-seidel spectral radius is 0.9887870 estimated iterations to convergence 77 setup time was (sec) 0.5400000 now iterating at: 21:10:31 rms-change max change #iterations 0.1829846 27.46126 at 10iterations 2.0533469E-02 2.676435 at 20iterations 2.4591710E-03 0.3617477 at 30iterations 3.3854690E-04 4.3831825E-02 at 40iterations 6.9930706E-05 9.1190338E-03 at 50iterations finished qdiffx linear iterations at : 21:10:34 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 6.9930706E-05 9.1190338E-03 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 21:10:35 4.416u 0.420s 0:05.20 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 Mon Oct 10 2011 at 21:10:35 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.040855 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): -23.99200 28.33900 ymin,ymax (A): -11.00300 30.80700 zmin,zma (A): -5.339000 46.72800 x,y,z range (A): 52.33100 41.81000 52.06700 scale (grids/A): 2.040855 object centre (A): 2.173500 9.902000 20.69450 number of atom coordinates read : 2386 total number of charged atoms : 2253 net assigned charge : 2.000021 assigned positive charge : 347.1422 centred at (gu) : 92.55443 87.37364 86.82678 assigned negative charge : -345.1430 centred at (gu) : 92.45920 87.55569 86.71815 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 81950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22187 grid for indexing accessible points = 1.400000 m= 31466 mr = 56035 m= 5989 mr = 23182 m= 488 mr = 3944 m= 9 mr = 199 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 324 time to turn everything in is 0.6700000 number of dielectric boundary points 36542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17839 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) : 0.6802852 object centre at (A) : 2.173500 9.902000 20.69450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2882179E-03 3.3744100E-02 midg,1,midg; midg,igrid,midg 3.4507136E-03 -2.1930428E-02 1,midg,midg; igrid,midg,midg 2.2660254E-02 3.8836740E-02 gauss-seidel spectral radius is 0.9987937 estimated iterations to convergence 228 setup time was (sec) 0.9800000 now iterating at: 21:10:36 rms-change max change #iterations 4.544302 181.9735 at 10iterations 2.225194 88.44576 at 20iterations 1.088716 32.74883 at 30iterations 0.5368413 16.63323 at 40iterations 0.2631244 7.779572 at 50iterations 0.1283767 3.995643 at 60iterations 6.3012540E-02 1.973038 at 70iterations 3.0971270E-02 0.9233780 at 80iterations 1.5126044E-02 0.4432564 at 90iterations 7.4523175E-03 0.2164135 at 100iterations 3.6580868E-03 0.1069336 at 110iterations 1.8075951E-03 5.2911758E-02 at 120iterations finished qdiffx linear iterations at : 21:10:47 total time elapsed so far: 11.54000 # loops : 120 mean,max change (kT/e) : 1.8075951E-03 5.2911758E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 21:10:47 11.700u 0.475s 0:12.43 97.9% 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 Mon Oct 10 2011 at 21:10:47 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.061283 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): -23.99200 28.33900 ymin,ymax (A): -11.00300 30.80700 zmin,zma (A): -5.339000 46.72800 x,y,z range (A): 52.33100 41.81000 52.06700 scale (grids/A): 3.061283 object centre (A): 2.173500 9.902000 20.69450 number of atom coordinates read : 2386 total number of charged atoms : 2253 net assigned charge : 2.000021 assigned positive charge : 347.1422 centred at (gu) : 93.83150 86.06030 85.24023 assigned negative charge : -345.1430 centred at (gu) : 93.68879 86.33350 85.07720 start vw surface at 0.1100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 188758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22187 grid for indexing accessible points = 1.400000 m= 98188 mr = 135484 m= 39421 mr = 79999 m= 11209 mr = 31764 m= 2152 mr = 8516 m= 181 mr = 1577 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 1115 time to turn everything in is 1.820000 number of dielectric boundary points 82482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 18024 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) : 2.040855 object centre at (A) : 2.173500 9.902000 20.69450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9844636E-02 0.5267874 midg,1,midg; midg,igrid,midg -6.9625914E-02 -0.2358529 1,midg,midg; igrid,midg,midg 0.3789258 0.4375403 gauss-seidel spectral radius is 0.9993064 estimated iterations to convergence 300 setup time was (sec) 2.170000 now iterating at: 21:10:50 rms-change max change #iterations 10.55221 520.6985 at 10iterations 6.284378 144.4734 at 20iterations 3.726290 77.36631 at 30iterations 2.209187 44.14359 at 40iterations 1.302615 32.23080 at 50iterations 0.7682078 20.88156 at 60iterations 0.4527636 7.964001 at 70iterations 0.2660496 4.976611 at 80iterations 0.1560649 2.760134 at 90iterations 9.1652907E-02 1.534739 at 100iterations 5.3670678E-02 0.9386841 at 110iterations 3.1437226E-02 0.5394115 at 120iterations 1.8410547E-02 0.3148670 at 130iterations 1.0836695E-02 0.2013655 at 140iterations 6.3768686E-03 0.1151867 at 150iterations 3.7665917E-03 6.4183950E-02 at 160iterations 2.2475726E-03 4.5566559E-02 at 170iterations 1.3542197E-03 2.3631096E-02 at 180iterations finished qdiffx linear iterations at : 21:11:06 total time elapsed so far: 18.30000 # loops : 180 mean,max change (kT/e) : 1.3542197E-03 2.3631096E-02 energy calculations done at 18.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.46000 DelPhi exited at 21:11:07 18.469u 0.465s 0:19.58 96.6% 0+0k 0+0io 0pf+0w