Wed Dec 21 14:21:33 PST 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 Wed Dec 21 2011 at 14:21:36 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6482628 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): -5.350000 34.70100 ymin,ymax (A): -3.375000 49.45700 zmin,zma (A): -8.035000 46.88100 x,y,z range (A): 40.05100 52.83200 54.91600 scale (grids/A): 0.6482628 object centre (A): 14.67550 23.04100 19.42300 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681008 assigned positive charge : 286.9481 centred at (gu) : 89.38810 92.09930 90.02292 assigned negative charge : -282.2673 centred at (gu) : 89.28943 92.23161 90.08084 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5626 nv = 96 ne = 84 npr = 40523 no. pairs analyzed = 40523 no. exposed pairs = 2511 no. arc points = 17615 no. surface atoms = 850 nbur = 1107 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3101 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2600000 number of dielectric boundary points 2773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1822 ## 203 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4982346E-08 2.8640361E-09 midg,1,midg; midg,igrid,midg 1.4671772E-08 -8.4943892E-09 1,midg,midg; igrid,midg,midg -1.7991511E-09 1.6953516E-08 gauss-seidel spectral radius is 0.9876130 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 14:21:38 rms-change max change #iterations 0.1300251 26.85774 at 10iterations 1.2982313E-02 2.170292 at 20iterations 1.3338914E-03 0.2032394 at 30iterations 1.3197918E-04 2.2094727E-02 at 40iterations 1.3199503E-05 2.1190643E-03 at 50iterations finished qdiffx linear iterations at : 14:21:43 total time elapsed so far: 6.150000 # loops : 50 mean,max change (kT/e) : 1.3199503E-05 2.1190643E-03 energy calculations done at 6.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.300000 DelPhi exited at 14:21:46 6.308u 0.510s 0:11.31 60.2% 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 Wed Dec 21 2011 at 14:21:49 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.944788 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): -5.350000 34.70100 ymin,ymax (A): -3.375000 49.45700 zmin,zma (A): -8.035000 46.88100 x,y,z range (A): 40.05100 52.83200 54.91600 scale (grids/A): 1.944788 object centre (A): 14.67550 23.04100 19.42300 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681008 assigned positive charge : 286.9481 centred at (gu) : 88.16441 96.29803 90.06888 assigned negative charge : -282.2673 centred at (gu) : 87.86842 96.69526 90.24265 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 60441 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17615 grid for indexing accessible points = 1.400000 m= 21457 mr = 41322 m= 3016 mr = 16157 m= 141 mr = 1956 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1108 time to turn everything in is 0.6200000 number of dielectric boundary points 25576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14390 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) : 0.6482628 object centre at (A) : 14.67550 23.04100 19.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5145380E-02 4.1924156E-02 midg,1,midg; midg,igrid,midg 3.5408404E-02 -5.8573419E-03 1,midg,midg; igrid,midg,midg 7.6093706E-03 9.1446666E-03 gauss-seidel spectral radius is 0.9986131 estimated iterations to convergence 213 setup time was (sec) 1.210000 now iterating at: 14:21:52 rms-change max change #iterations 3.700898 186.6531 at 10iterations 1.725674 63.75426 at 20iterations 0.8028067 30.45874 at 30iterations 0.3737761 13.46717 at 40iterations 0.1735822 6.202669 at 50iterations 8.0682963E-02 2.790924 at 60iterations 3.7538424E-02 1.305921 at 70iterations 1.7512491E-02 0.6223578 at 80iterations 8.1114136E-03 0.2893836 at 90iterations 3.7807608E-03 0.1433330 at 100iterations 1.7496343E-03 6.0880661E-02 at 110iterations 8.1861304E-04 3.0687332E-02 at 120iterations finished qdiffx linear iterations at : 14:22:02 total time elapsed so far: 11.43000 # loops : 120 mean,max change (kT/e) : 8.1861304E-04 3.0687332E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 14:22:07 11.597u 0.910s 0:18.57 67.3% 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 Wed Dec 21 2011 at 14:22:08 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1957 !!! WARNING: ASH 125 has a net charge of -0.3190 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: 2.917183 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): -5.350000 34.70100 ymin,ymax (A): -3.375000 49.45700 zmin,zma (A): -8.035000 46.88100 x,y,z range (A): 40.05100 52.83200 54.91600 scale (grids/A): 2.917183 object centre (A): 14.67550 23.04100 19.42300 number of atom coordinates read : 1957 total number of charged atoms : 1824 net assigned charge : 4.681008 assigned positive charge : 286.9481 centred at (gu) : 87.24670 99.44695 90.10342 assigned negative charge : -282.2673 centred at (gu) : 86.80257 100.0429 90.36400 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 139475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17615 grid for indexing accessible points = 1.400000 m= 69952 mr = 99892 m= 24680 mr = 57799 m= 5381 mr = 20264 m= 644 mr = 4065 m= 26 mr = 442 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 3765 time to turn everything in is 1.550000 number of dielectric boundary points 57689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 14587 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) : 1.944788 object centre at (A) : 14.67550 23.04100 19.42300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4060311E-02 0.8545305 midg,1,midg; midg,igrid,midg 0.3593029 -0.1111793 1,midg,midg; igrid,midg,midg 0.1439195 5.8486771E-02 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 2.120000 now iterating at: 14:22:11 rms-change max change #iterations 8.653311 355.7581 at 10iterations 5.000774 137.0186 at 20iterations 2.857333 71.21944 at 30iterations 1.637442 47.13380 at 40iterations 0.9351937 20.20573 at 50iterations 0.5354771 11.70287 at 60iterations 0.3043659 6.498741 at 70iterations 0.1730685 3.948290 at 80iterations 9.9069260E-02 2.225508 at 90iterations 5.6272835E-02 1.133314 at 100iterations 3.2094773E-02 0.6168060 at 110iterations 1.8273842E-02 0.3742294 at 120iterations 1.0412457E-02 0.2110002 at 130iterations 5.9456248E-03 0.1209652 at 140iterations 3.3849294E-03 6.6650391E-02 at 150iterations 1.9213741E-03 3.6198378E-02 at 160iterations 1.0991608E-03 2.2314072E-02 at 170iterations 6.2363484E-04 1.2200832E-02 at 180iterations finished qdiffx linear iterations at : 14:22:36 total time elapsed so far: 26.86000 # loops : 180 mean,max change (kT/e) : 6.2363484E-04 1.2200832E-02 energy calculations done at 26.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 27.03000 DelPhi exited at 14:22:39 27.034u 0.972s 0:32.46 86.2% 0+0k 0+0io 0pf+0w