Mon Oct 10 23:52:22 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 23:52:22 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 = 2631 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: 0.5844689 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): 10.40200 64.78800 ymin,ymax (A): -1.271000 59.63900 zmin,zma (A): 10.34000 54.00600 x,y,z range (A): 54.38600 60.91000 43.66600 scale (grids/A): 0.5844689 object centre (A): 37.59500 29.18400 32.17300 number of atom coordinates read : 2631 total number of charged atoms : 2491 net assigned charge : 9.000021 assigned positive charge : 396.4807 centred at (gu) : 88.67057 90.59164 89.60832 assigned negative charge : -387.4814 centred at (gu) : 88.67635 90.48452 89.73035 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5828 nv = 96 ne = 84 npr = 52935 no. pairs analyzed = 52935 no. exposed pairs = 3175 no. arc points = 21928 no. surface atoms = 1063 nbur = 1568 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 254 mr = 3216 m= 0 mr = 13 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.3500000 number of dielectric boundary points 2853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2217 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4011915E-09 -4.3141507E-10 midg,1,midg; midg,igrid,midg -1.1134688E-10 5.2880598E-09 1,midg,midg; igrid,midg,midg 3.2352434E-09 1.5884867E-09 gauss-seidel spectral radius is 0.9848551 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 23:52:23 rms-change max change #iterations 9.6510425E-02 16.75528 at 10iterations 8.8672610E-03 1.497913 at 20iterations 1.2465287E-03 0.2925034 at 30iterations 3.1518226E-04 7.9494476E-02 at 40iterations 8.6503969E-05 2.1995544E-02 at 50iterations finished qdiffx linear iterations at : 23:52:26 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 8.6503969E-05 2.1995544E-02 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 23:52:27 4.202u 0.243s 0:04.87 91.1% 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 23:52:27 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 = 2631 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: 1.753407 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): 10.40200 64.78800 ymin,ymax (A): -1.271000 59.63900 zmin,zma (A): 10.34000 54.00600 x,y,z range (A): 54.38600 60.91000 43.66600 scale (grids/A): 1.753407 object centre (A): 37.59500 29.18400 32.17300 number of atom coordinates read : 2631 total number of charged atoms : 2491 net assigned charge : 9.000021 assigned positive charge : 396.4807 centred at (gu) : 86.01098 91.77435 88.82447 assigned negative charge : -387.4814 centred at (gu) : 86.02852 91.45314 89.19057 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64161 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21928 grid for indexing accessible points = 1.400000 m= 21266 mr = 44636 m= 2589 mr = 15614 m= 76 mr = 1515 m= 0 mr = 18 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1838 time to turn everything in is 0.5600000 number of dielectric boundary points 26309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19385 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) : 0.5844689 object centre at (A) : 37.59500 29.18400 32.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3765728E-02 3.6364691E-03 midg,1,midg; midg,igrid,midg -8.3964420E-03 -1.3814815E-02 1,midg,midg; igrid,midg,midg 4.9191439E-03 1.2583520E-02 gauss-seidel spectral radius is 0.9983897 estimated iterations to convergence 198 setup time was (sec) 0.8700000 now iterating at: 23:52:28 rms-change max change #iterations 3.568771 160.4546 at 10iterations 1.567549 58.68573 at 20iterations 0.6855209 25.82591 at 30iterations 0.3016855 10.39189 at 40iterations 0.1326398 5.100590 at 50iterations 5.8577005E-02 1.989594 at 60iterations 2.5825471E-02 0.8845615 at 70iterations 1.1476231E-02 0.4225979 at 80iterations 5.1755607E-03 0.1962409 at 90iterations 2.4249053E-03 0.1031647 at 100iterations 1.2025486E-03 4.9316406E-02 at 110iterations 6.3745648E-04 3.1497955E-02 at 120iterations finished qdiffx linear iterations at : 23:52:36 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 6.3745648E-04 3.1497955E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 23:52:37 9.365u 0.258s 0:10.23 93.9% 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 23:52:37 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 = 2631 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: 2.630110 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): 10.40200 64.78800 ymin,ymax (A): -1.271000 59.63900 zmin,zma (A): 10.34000 54.00600 x,y,z range (A): 54.38600 60.91000 43.66600 scale (grids/A): 2.630110 object centre (A): 37.59500 29.18400 32.17300 number of atom coordinates read : 2631 total number of charged atoms : 2491 net assigned charge : 9.000021 assigned positive charge : 396.4807 centred at (gu) : 84.01635 92.66142 88.23660 assigned negative charge : -387.4814 centred at (gu) : 84.04280 92.17969 88.78577 start vw surface at 0.1800000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 148834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21928 grid for indexing accessible points = 1.400000 m= 71367 mr = 108655 m= 22905 mr = 58210 m= 4363 mr = 18305 m= 404 mr = 3206 m= 12 mr = 211 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 6362 time to turn everything in is 1.270000 number of dielectric boundary points 59293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 19922 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) : 1.753407 object centre at (A) : 37.59500 29.18400 32.17300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2990031 6.1173443E-02 midg,1,midg; midg,igrid,midg -0.3170409 -0.5211965 1,midg,midg; igrid,midg,midg 5.1247706E-03 0.1112887 gauss-seidel spectral radius is 0.9991831 estimated iterations to convergence 276 setup time was (sec) 1.610000 now iterating at: 23:52:39 rms-change max change #iterations 8.716577 267.2679 at 10iterations 4.892498 120.5089 at 20iterations 2.742666 56.06571 at 30iterations 1.538952 30.65158 at 40iterations 0.8611110 18.10939 at 50iterations 0.4800667 9.113777 at 60iterations 0.2683010 5.797127 at 70iterations 0.1498143 3.038587 at 80iterations 8.3689004E-02 1.779129 at 90iterations 4.6795398E-02 0.9204748 at 100iterations 2.6252331E-02 0.5871887 at 110iterations 1.4736281E-02 0.3309631 at 120iterations 8.3373655E-03 0.1707344 at 130iterations 4.7295159E-03 0.1016006 at 140iterations 2.7462167E-03 6.8604469E-02 at 150iterations 1.6458310E-03 4.2106628E-02 at 160iterations 1.0290224E-03 2.8045654E-02 at 170iterations 6.7658012E-04 2.0084381E-02 at 180iterations finished qdiffx linear iterations at : 23:52:52 total time elapsed so far: 14.57000 # loops : 180 mean,max change (kT/e) : 6.7658012E-04 2.0084381E-02 energy calculations done at 14.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.75000 DelPhi exited at 23:52:53 14.749u 0.252s 0:15.35 97.6% 0+0k 0+0io 0pf+0w