Mon Oct 10 19:36:56 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 Mon Oct 10 2011 at 19:36:56 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 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: 0.6767288 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): -17.15800 35.44800 ymin,ymax (A): -7.267000 37.63100 zmin,zma (A): -2.192000 48.91600 x,y,z range (A): 52.60600 44.89800 51.10800 scale (grids/A): 0.6767288 object centre (A): 9.145000 15.18200 23.36200 number of atom coordinates read : 2400 total number of charged atoms : 2264 net assigned charge : 0.5000051 assigned positive charge : 359.1549 centred at (gu) : 92.38473 90.58831 91.04471 assigned negative charge : -358.6555 centred at (gu) : 92.28386 90.77794 91.10896 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7635 nv = 96 ne = 84 npr = 48043 no. pairs analyzed = 48043 no. exposed pairs = 3245 no. arc points = 22120 no. surface atoms = 1086 nbur = 1314 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 571 mr = 4189 m= 5 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3100000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8603 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5689801E-08 -1.9915552E-08 midg,1,midg; midg,igrid,midg 4.7033648E-08 -5.8209192E-08 1,midg,midg; igrid,midg,midg -1.6073910E-08 4.8439940E-08 gauss-seidel spectral radius is 0.9886683 estimated iterations to convergence 77 setup time was (sec) 0.5700000 now iterating at: 19:36:56 rms-change max change #iterations 0.1767053 28.50074 at 10iterations 1.9840587E-02 3.054404 at 20iterations 2.3618727E-03 0.3345909 at 30iterations 3.7850850E-04 5.6018710E-02 at 40iterations 1.0474266E-04 1.5745163E-02 at 50iterations finished qdiffx linear iterations at : 19:36:59 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 1.0474266E-04 1.5745163E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 19:37:00 3.630u 0.209s 0:04.25 90.1% 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 Mon Oct 10 2011 at 19:37:00 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 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: 2.030187 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): -17.15800 35.44800 ymin,ymax (A): -7.267000 37.63100 zmin,zma (A): -2.192000 48.91600 x,y,z range (A): 52.60600 44.89800 51.10800 scale (grids/A): 2.030187 object centre (A): 9.145000 15.18200 23.36200 number of atom coordinates read : 2400 total number of charged atoms : 2264 net assigned charge : 0.5000051 assigned positive charge : 359.1549 centred at (gu) : 97.15372 91.76443 93.13337 assigned negative charge : -358.6555 centred at (gu) : 96.85135 92.33388 93.32669 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22120 grid for indexing accessible points = 1.400000 m= 32865 mr = 56083 m= 6718 mr = 24437 m= 646 mr = 4344 m= 18 mr = 312 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1854 time to turn everything in is 0.6600000 number of dielectric boundary points 36226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17949 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) : 0.6767288 object centre at (A) : 9.145000 15.18200 23.36200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7370168E-02 2.5206953E-03 midg,1,midg; midg,igrid,midg 2.6458971E-02 -1.3520454E-02 1,midg,midg; igrid,midg,midg -1.2912709E-02 1.7594814E-02 gauss-seidel spectral radius is 0.9987775 estimated iterations to convergence 226 setup time was (sec) 0.9800000 now iterating at: 19:37:01 rms-change max change #iterations 4.610276 204.1396 at 10iterations 2.234388 76.79842 at 20iterations 1.092301 33.80748 at 30iterations 0.5314859 15.31400 at 40iterations 0.2596404 7.616292 at 50iterations 0.1266122 3.952505 at 60iterations 6.1974503E-02 2.055511 at 70iterations 3.0204745E-02 1.021528 at 80iterations 1.4759381E-02 0.4108295 at 90iterations 7.2038076E-03 0.1987782 at 100iterations 3.5417983E-03 0.1061110 at 110iterations 1.7510247E-03 5.3899765E-02 at 120iterations finished qdiffx linear iterations at : 19:37:08 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 1.7510247E-03 5.3899765E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 19:37:09 8.402u 0.227s 0:08.94 96.4% 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 19:37:09 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 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: 3.045280 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): -17.15800 35.44800 ymin,ymax (A): -7.267000 37.63100 zmin,zma (A): -2.192000 48.91600 x,y,z range (A): 52.60600 44.89800 51.10800 scale (grids/A): 3.045280 object centre (A): 9.145000 15.18200 23.36200 number of atom coordinates read : 2400 total number of charged atoms : 2264 net assigned charge : 0.5000051 assigned positive charge : 359.1549 centred at (gu) : 100.7303 92.64645 94.69987 assigned negative charge : -358.6555 centred at (gu) : 100.2770 93.50078 94.98999 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 187140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22120 grid for indexing accessible points = 1.400000 m= 100930 mr = 135826 m= 42650 mr = 82535 m= 12445 mr = 34616 m= 2495 mr = 9261 m= 296 mr = 1786 m= 7 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 5972 time to turn everything in is 1.670000 number of dielectric boundary points 81760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 18112 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) : 2.030187 object centre at (A) : 9.145000 15.18200 23.36200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4499448 0.4404034 midg,1,midg; midg,igrid,midg 0.2015481 4.9852815E-02 1,midg,midg; igrid,midg,midg -5.2115180E-02 7.5291372E-03 gauss-seidel spectral radius is 0.9992956 estimated iterations to convergence 297 setup time was (sec) 2.000000 now iterating at: 19:37:11 rms-change max change #iterations 10.68193 459.8582 at 10iterations 6.346858 142.0465 at 20iterations 3.769016 83.32215 at 30iterations 2.231122 43.02868 at 40iterations 1.315207 26.19534 at 50iterations 0.7741940 15.67353 at 60iterations 0.4541341 9.365334 at 70iterations 0.2668445 5.696020 at 80iterations 0.1558347 2.654877 at 90iterations 9.1436967E-02 1.591728 at 100iterations 5.3309221E-02 0.8922663 at 110iterations 3.1138403E-02 0.5485229 at 120iterations 1.8240554E-02 0.3003902 at 130iterations 1.0634311E-02 0.1931553 at 140iterations 6.2212809E-03 0.1039524 at 150iterations 3.6363248E-03 5.9434414E-02 at 160iterations 2.1331809E-03 3.5892487E-02 at 170iterations 1.2544160E-03 2.3532867E-02 at 180iterations finished qdiffx linear iterations at : 19:37:21 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 1.2544160E-03 2.3532867E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 19:37:22 12.534u 0.237s 0:13.07 97.6% 0+0k 0+0io 0pf+0w