Sat Oct 8 21:48:30 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 Sat Oct 8 2011 at 21:48:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 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: 0.6592226 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): -5.802000 42.83500 ymin,ymax (A): -21.22200 32.78100 zmin,zma (A): 2.752000 55.13700 x,y,z range (A): 48.63700 54.00300 52.38500 scale (grids/A): 0.6592226 object centre (A): 18.51650 5.779501 28.94450 number of atom coordinates read : 2526 total number of charged atoms : 2388 net assigned charge : 4.000006 assigned positive charge : 378.2159 centred at (gu) : 88.94810 89.23588 91.91674 assigned negative charge : -374.2164 centred at (gu) : 88.96455 89.24736 91.87342 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7504 nv = 96 ne = 84 npr = 50637 no. pairs analyzed = 50637 no. exposed pairs = 3120 no. arc points = 21982 no. surface atoms = 1053 nbur = 1473 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4119 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8706 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2058492E-09 2.6384868E-08 midg,1,midg; midg,igrid,midg 1.3795296E-08 6.4871482E-09 1,midg,midg; igrid,midg,midg 1.5788775E-08 5.3902722E-09 gauss-seidel spectral radius is 0.9880694 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 21:48:31 rms-change max change #iterations 0.1605370 21.65867 at 10iterations 1.7562982E-02 2.506443 at 20iterations 1.8550479E-03 0.2800827 at 30iterations 2.2525516E-04 3.0761719E-02 at 40iterations 4.1619329E-05 5.1975250E-03 at 50iterations finished qdiffx linear iterations at : 21:48:34 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 4.1619329E-05 5.1975250E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 21:48:34 3.521u 0.229s 0:04.02 93.0% 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 21:48:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 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: 1.977668 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): -5.802000 42.83500 ymin,ymax (A): -21.22200 32.78100 zmin,zma (A): 2.752000 55.13700 x,y,z range (A): 48.63700 54.00300 52.38500 scale (grids/A): 1.977668 object centre (A): 18.51650 5.779501 28.94450 number of atom coordinates read : 2526 total number of charged atoms : 2388 net assigned charge : 4.000006 assigned positive charge : 378.2159 centred at (gu) : 86.84353 87.70722 95.74966 assigned negative charge : -374.2164 centred at (gu) : 86.89339 87.74191 95.61986 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 80674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21982 grid for indexing accessible points = 1.400000 m= 30648 mr = 56603 m= 5350 mr = 22338 m= 458 mr = 3320 m= 9 mr = 207 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 34671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 18868 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) : 0.6592226 object centre at (A) : 18.51650 5.779501 28.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5823919E-02 3.0459246E-02 midg,1,midg; midg,igrid,midg -2.1220859E-02 -2.8397642E-02 1,midg,midg; igrid,midg,midg 3.8540341E-02 1.8427033E-02 gauss-seidel spectral radius is 0.9987275 estimated iterations to convergence 222 setup time was (sec) 0.8700000 now iterating at: 21:48:36 rms-change max change #iterations 4.497531 211.3354 at 10iterations 2.171469 75.03616 at 20iterations 1.042230 33.70279 at 30iterations 0.5028312 17.01495 at 40iterations 0.2424054 8.055878 at 50iterations 0.1166245 3.489571 at 60iterations 5.6019761E-02 1.744404 at 70iterations 2.6960768E-02 0.8547401 at 80iterations 1.2990797E-02 0.4154854 at 90iterations 6.2432201E-03 0.1821518 at 100iterations 3.0237448E-03 9.0665489E-02 at 110iterations 1.4543994E-03 4.3203831E-02 at 120iterations finished qdiffx linear iterations at : 21:48:43 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.4543994E-03 4.3203831E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 21:48:43 8.053u 0.296s 0:08.67 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 21:48:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2526 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: 2.966502 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): -5.802000 42.83500 ymin,ymax (A): -21.22200 32.78100 zmin,zma (A): 2.752000 55.13700 x,y,z range (A): 48.63700 54.00300 52.38500 scale (grids/A): 2.966502 object centre (A): 18.51650 5.779501 28.94450 number of atom coordinates read : 2526 total number of charged atoms : 2388 net assigned charge : 4.000006 assigned positive charge : 378.2159 centred at (gu) : 85.26528 86.56084 98.62436 assigned negative charge : -374.2164 centred at (gu) : 85.34003 86.61279 98.42974 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 186285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21982 grid for indexing accessible points = 1.400000 m= 97781 mr = 136825 m= 36889 mr = 80103 m= 9881 mr = 29084 m= 1858 mr = 7256 m= 171 mr = 1310 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 78197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19104 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) : 1.977668 object centre at (A) : 18.51650 5.779501 28.94450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3346442 0.3042022 midg,1,midg; midg,igrid,midg -0.5446606 -0.5065932 1,midg,midg; igrid,midg,midg 0.4970749 8.4026068E-02 gauss-seidel spectral radius is 0.9992942 estimated iterations to convergence 297 setup time was (sec) 1.730000 now iterating at: 21:48:45 rms-change max change #iterations 10.55356 382.0569 at 10iterations 6.304088 147.8258 at 20iterations 3.747074 81.73277 at 30iterations 2.219777 47.87117 at 40iterations 1.308941 26.99163 at 50iterations 0.7712852 14.05889 at 60iterations 0.4533458 8.767204 at 70iterations 0.2653630 5.040047 at 80iterations 0.1556026 2.772005 at 90iterations 9.0896703E-02 1.658390 at 100iterations 5.3279057E-02 0.9404602 at 110iterations 3.1101963E-02 0.5761151 at 120iterations 1.8125175E-02 0.2986779 at 130iterations 1.0592817E-02 0.1930714 at 140iterations 6.1981259E-03 0.1144934 at 150iterations 3.6152133E-03 7.8175545E-02 at 160iterations 2.1094836E-03 4.0109634E-02 at 170iterations 1.2322355E-03 2.1175861E-02 at 180iterations finished qdiffx linear iterations at : 21:48:55 total time elapsed so far: 11.29000 # loops : 180 mean,max change (kT/e) : 1.2322355E-03 2.1175861E-02 energy calculations done at 11.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.48000 DelPhi exited at 21:48:55 11.483u 0.183s 0:11.93 97.7% 0+0k 0+0io 0pf+0w