Mon Oct 10 14:01:59 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 14:01:59 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2095 !!! WARNING: HIR 79 has a net charge of 0.5140 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: 0.6126418 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): -10.10200 34.04500 ymin,ymax (A): 7.549000 49.57400 zmin,zma (A): 34.89800 93.00700 x,y,z range (A): 44.14700 42.02500 58.10900 scale (grids/A): 0.6126418 object centre (A): 11.97150 28.56150 63.95250 number of atom coordinates read : 2095 total number of charged atoms : 1963 net assigned charge : -2.485998 assigned positive charge : 276.5631 centred at (gu) : 91.91503 90.15125 90.85921 assigned negative charge : -279.0493 centred at (gu) : 91.83010 90.17014 91.15895 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5505 nv = 96 ne = 84 npr = 44097 no. pairs analyzed = 44097 no. exposed pairs = 2843 no. arc points = 20539 no. surface atoms = 971 nbur = 1124 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2671 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1856 ## 102 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8779738E-09 -1.6295234E-08 midg,1,midg; midg,igrid,midg -7.7766910E-10 -2.3244164E-09 1,midg,midg; igrid,midg,midg -3.1519489E-09 2.6922604E-09 gauss-seidel spectral radius is 0.9861780 estimated iterations to convergence 70 setup time was (sec) 0.7200000 now iterating at: 14:02:00 rms-change max change #iterations 0.1000756 18.03048 at 10iterations 9.1710510E-03 1.666704 at 20iterations 8.4660802E-04 0.1282573 at 30iterations 1.1514477E-04 2.0778656E-02 at 40iterations 2.5244914E-05 4.3659210E-03 at 50iterations finished qdiffx linear iterations at : 14:02:06 total time elapsed so far: 6.570000 # loops : 50 mean,max change (kT/e) : 2.5244914E-05 4.3659210E-03 energy calculations done at 6.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.750000 DelPhi exited at 14:02:07 6.753u 0.645s 0:08.45 87.4% 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 14:02:08 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2095 !!! WARNING: HIR 79 has a net charge of 0.5140 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: 1.837925 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): -10.10200 34.04500 ymin,ymax (A): 7.549000 49.57400 zmin,zma (A): 34.89800 93.00700 x,y,z range (A): 44.14700 42.02500 58.10900 scale (grids/A): 1.837925 object centre (A): 11.97150 28.56150 63.95250 number of atom coordinates read : 2095 total number of charged atoms : 1963 net assigned charge : -2.485998 assigned positive charge : 276.5631 centred at (gu) : 95.74508 90.45396 92.57773 assigned negative charge : -279.0493 centred at (gu) : 95.49061 90.51050 93.47691 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20539 grid for indexing accessible points = 1.400000 m= 19764 mr = 38762 m= 2958 mr = 13337 m= 157 mr = 1579 m= 0 mr = 41 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 28625 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15430 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) : 0.6126418 object centre at (A) : 11.97150 28.56150 63.95250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2383088E-02 -6.7977153E-02 midg,1,midg; midg,igrid,midg 3.5450298E-03 1.8744138E-03 1,midg,midg; igrid,midg,midg -6.2632263E-03 6.9797121E-04 gauss-seidel spectral radius is 0.9985068 estimated iterations to convergence 205 setup time was (sec) 1.030000 now iterating at: 14:02:09 rms-change max change #iterations 3.327491 182.9190 at 10iterations 1.498406 92.25605 at 20iterations 0.6785414 26.69759 at 30iterations 0.3067558 11.78911 at 40iterations 0.1390756 5.816689 at 50iterations 6.2917277E-02 2.302177 at 60iterations 2.8445315E-02 1.058558 at 70iterations 1.2936756E-02 0.4900737 at 80iterations 5.8310777E-03 0.2020721 at 90iterations 2.6499468E-03 0.1103020 at 100iterations 1.1979199E-03 4.3176651E-02 at 110iterations 5.4482894E-04 2.0845413E-02 at 120iterations finished qdiffx linear iterations at : 14:02:25 total time elapsed so far: 16.34000 # loops : 120 mean,max change (kT/e) : 5.4482894E-04 2.0845413E-02 energy calculations done at 16.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.52000 DelPhi exited at 14:02:25 16.521u 0.753s 0:17.70 97.5% 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 14:02:25 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2095 !!! WARNING: HIR 79 has a net charge of 0.5140 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: 2.756888 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): -10.10200 34.04500 ymin,ymax (A): 7.549000 49.57400 zmin,zma (A): 34.89800 93.00700 x,y,z range (A): 44.14700 42.02500 58.10900 scale (grids/A): 2.756888 object centre (A): 11.97150 28.56150 63.95250 number of atom coordinates read : 2095 total number of charged atoms : 1963 net assigned charge : -2.485998 assigned positive charge : 276.5631 centred at (gu) : 98.61766 90.68091 93.86655 assigned negative charge : -279.0493 centred at (gu) : 98.23600 90.76591 95.21544 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 137427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20539 grid for indexing accessible points = 1.400000 m= 63863 mr = 94505 m= 22414 mr = 49715 m= 5087 mr = 16860 m= 621 mr = 3433 m= 26 mr = 368 m= 0 mr = 8 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.410000 number of dielectric boundary points 64549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 15700 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) : 1.837925 object centre at (A) : 11.97150 28.56150 63.95250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3189911 -0.7675412 midg,1,midg; midg,igrid,midg 2.9438591E-02 1.6317304E-02 1,midg,midg; igrid,midg,midg -4.8483856E-02 5.0133222E-04 gauss-seidel spectral radius is 0.9992259 estimated iterations to convergence 284 setup time was (sec) 1.910000 now iterating at: 14:02:28 rms-change max change #iterations 7.982004 308.5873 at 10iterations 4.642339 129.4558 at 20iterations 2.662058 70.01855 at 30iterations 1.526946 34.01722 at 40iterations 0.8723872 21.75978 at 50iterations 0.4994162 11.12674 at 60iterations 0.2838612 5.857200 at 70iterations 0.1619491 3.582439 at 80iterations 9.1942899E-02 1.909829 at 90iterations 5.2349765E-02 1.047253 at 100iterations 2.9725192E-02 0.6328988 at 110iterations 1.6902721E-02 0.3538895 at 120iterations 9.5885107E-03 0.2088227 at 130iterations 5.4614544E-03 0.1121941 at 140iterations 3.1131874E-03 6.1620712E-02 at 150iterations 1.7735838E-03 3.5056412E-02 at 160iterations 1.0192458E-03 2.1614075E-02 at 170iterations 5.9013389E-04 1.3258457E-02 at 180iterations finished qdiffx linear iterations at : 14:02:53 total time elapsed so far: 26.61000 # loops : 180 mean,max change (kT/e) : 5.9013389E-04 1.3258457E-02 energy calculations done at 26.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.77000 DelPhi exited at 14:02:53 26.774u 0.812s 0:28.13 98.0% 0+0k 0+0io 0pf+0w