Mon Oct 10 14:00:30 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+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 14:00:30 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 !!! WARNING: HIR 88 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6472256 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): 6.400000 58.99500 ymin,ymax (A): 22.00100 77.00500 zmin,zma (A): -8.432000 40.48700 x,y,z range (A): 52.59500 55.00401 48.91900 scale (grids/A): 0.6472256 object centre (A): 32.69750 49.50300 16.02750 number of atom coordinates read : 2550 total number of charged atoms : 2413 net assigned charge : 6.514017 assigned positive charge : 384.9409 centred at (gu) : 92.66567 89.55235 88.15894 assigned negative charge : -378.4275 centred at (gu) : 92.61022 89.52036 88.18147 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7299 nv = 96 ne = 84 npr = 50914 no. pairs analyzed = 50914 no. exposed pairs = 3298 no. arc points = 23320 no. surface atoms = 1105 nbur = 1445 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 391 mr = 3880 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1020551E-08 5.6729821E-09 midg,1,midg; midg,igrid,midg 7.4890565E-09 1.4217009E-08 1,midg,midg; igrid,midg,midg 2.2603184E-09 3.3048611E-08 gauss-seidel spectral radius is 0.9876294 estimated iterations to convergence 73 setup time was (sec) 0.4200000 now iterating at: 14:00:31 rms-change max change #iterations 0.1517417 25.25945 at 10iterations 1.5737033E-02 2.271965 at 20iterations 1.6583403E-03 0.2318668 at 30iterations 2.3180267E-04 3.8907051E-02 at 40iterations 6.0683094E-05 8.7008476E-03 at 50iterations finished qdiffx linear iterations at : 14:00:34 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 6.0683094E-05 8.7008476E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:00:35 3.662u 0.233s 0:04.89 79.5% 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 14:00:35 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 !!! WARNING: HIR 88 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.941677 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): 6.400000 58.99500 ymin,ymax (A): 22.00100 77.00500 zmin,zma (A): -8.432000 40.48700 x,y,z range (A): 52.59500 55.00401 48.91900 scale (grids/A): 1.941677 object centre (A): 32.69750 49.50300 16.02750 number of atom coordinates read : 2550 total number of charged atoms : 2413 net assigned charge : 6.514017 assigned positive charge : 384.9409 centred at (gu) : 97.99648 88.65661 84.47644 assigned negative charge : -378.4275 centred at (gu) : 97.83057 88.56085 84.54411 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 78535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23320 grid for indexing accessible points = 1.400000 m= 28418 mr = 53908 m= 4578 mr = 20290 m= 322 mr = 2711 m= 6 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 34849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 18995 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) : 0.6472256 object centre at (A) : 32.69750 49.50300 16.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3020607E-03 -1.2660106E-02 midg,1,midg; midg,igrid,midg -2.5315065E-02 4.0833537E-02 1,midg,midg; igrid,midg,midg 2.8970253E-02 3.9990988E-02 gauss-seidel spectral radius is 0.9986815 estimated iterations to convergence 218 setup time was (sec) 0.6300000 now iterating at: 14:00:36 rms-change max change #iterations 4.390629 171.5100 at 10iterations 2.075028 66.28625 at 20iterations 0.9865440 31.71338 at 30iterations 0.4686012 14.58327 at 40iterations 0.2227834 7.510877 at 50iterations 0.1057453 3.460151 at 60iterations 5.0268687E-02 1.775639 at 70iterations 2.3911202E-02 0.8147526 at 80iterations 1.1299161E-02 0.3949661 at 90iterations 5.3765923E-03 0.1563601 at 100iterations 2.5526441E-03 9.1541290E-02 at 110iterations 1.2204524E-03 3.5268307E-02 at 120iterations finished qdiffx linear iterations at : 14:00:44 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 1.2204524E-03 3.5268307E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 14:00:44 8.294u 0.236s 0:08.96 95.0% 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 Mon Oct 10 2011 at 14:00:44 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2550 !!! WARNING: HIR 88 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.912515 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): 6.400000 58.99500 ymin,ymax (A): 22.00100 77.00500 zmin,zma (A): -8.432000 40.48700 x,y,z range (A): 52.59500 55.00401 48.91900 scale (grids/A): 2.912515 object centre (A): 32.69750 49.50300 16.02750 number of atom coordinates read : 2550 total number of charged atoms : 2413 net assigned charge : 6.514017 assigned positive charge : 384.9409 centred at (gu) : 101.9947 87.98463 81.71449 assigned negative charge : -378.4275 centred at (gu) : 101.7457 87.84118 81.81618 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 181175 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23320 grid for indexing accessible points = 1.400000 m= 91657 mr = 130667 m= 33364 mr = 74002 m= 8246 mr = 25917 m= 1261 mr = 5891 m= 78 mr = 800 m= 0 mr = 21 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 78483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 19304 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) : 1.941677 object centre at (A) : 32.69750 49.50300 16.02750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1951939E-02 -0.1823959 midg,1,midg; midg,igrid,midg -0.8901862 0.4003724 1,midg,midg; igrid,midg,midg 0.2952400 0.3415809 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 1.270000 now iterating at: 14:00:46 rms-change max change #iterations 10.34872 314.0470 at 10iterations 6.152833 131.8640 at 20iterations 3.653936 90.16577 at 30iterations 2.152325 46.57494 at 40iterations 1.264677 27.03433 at 50iterations 0.7411727 15.59431 at 60iterations 0.4328772 8.185439 at 70iterations 0.2519322 4.590584 at 80iterations 0.1469349 3.141129 at 90iterations 8.5745148E-02 1.678013 at 100iterations 4.9833100E-02 0.9407444 at 110iterations 2.9017424E-02 0.5277185 at 120iterations 1.6856860E-02 0.2968626 at 130iterations 9.8074879E-03 0.2097130 at 140iterations 5.7019694E-03 0.1125703 at 150iterations 3.3229585E-03 6.5419197E-02 at 160iterations 1.9394589E-03 3.3264160E-02 at 170iterations 1.1372786E-03 2.1485329E-02 at 180iterations finished qdiffx linear iterations at : 14:00:58 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 1.1372786E-03 2.1485329E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 14:00:59 12.954u 0.251s 0:14.08 93.7% 0+0k 0+0io 0pf+0w