Sun Oct 9 06:30:45 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 Sun Oct 9 2011 at 06:30:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 300 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6627942 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): 1.878000 44.32300 ymin,ymax (A): -9.236000 36.95000 zmin,zma (A): -25.14500 28.56700 x,y,z range (A): 42.44500 46.18600 53.71200 scale (grids/A): 0.6627942 object centre (A): 23.10050 13.85700 1.710999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.8980 centred at (gu) : 89.88771 89.48821 88.79195 assigned negative charge : -301.3981 centred at (gu) : 89.74152 89.31651 88.73584 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5947 nv = 96 ne = 84 npr = 41414 no. pairs analyzed = 41414 no. exposed pairs = 2404 no. arc points = 17438 no. surface atoms = 811 nbur = 1183 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 316 mr = 3285 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.1700000 number of dielectric boundary points 2916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1703 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0277112E-08 2.0296820E-09 midg,1,midg; midg,igrid,midg -3.9280081E-08 1.9085254E-08 1,midg,midg; igrid,midg,midg -3.1663600E-08 1.6822911E-08 gauss-seidel spectral radius is 0.9881451 estimated iterations to convergence 75 setup time was (sec) 0.3500000 now iterating at: 06:30:46 rms-change max change #iterations 0.1456619 21.31600 at 10iterations 1.5513453E-02 2.460510 at 20iterations 1.6462029E-03 0.2755165 at 30iterations 1.7740307E-04 2.7361870E-02 at 40iterations 1.8739096E-05 2.6106834E-03 at 50iterations finished qdiffx linear iterations at : 06:30:49 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.8739096E-05 2.6106834E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:30:49 3.323u 0.171s 0:03.89 89.7% 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 Sun Oct 9 2011 at 06:30:49 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 300 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.988383 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): 1.878000 44.32300 ymin,ymax (A): -9.236000 36.95000 zmin,zma (A): -25.14500 28.56700 x,y,z range (A): 42.44500 46.18600 53.71200 scale (grids/A): 1.988383 object centre (A): 23.10050 13.85700 1.710999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.8980 centred at (gu) : 89.66337 88.46478 86.37589 assigned negative charge : -301.3981 centred at (gu) : 89.22469 87.94967 86.20736 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17438 grid for indexing accessible points = 1.400000 m= 23521 mr = 43484 m= 4087 mr = 17846 m= 342 mr = 2742 m= 6 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 635 time to turn everything in is 0.3300000 number of dielectric boundary points 26804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14682 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) : 0.6627942 object centre at (A) : 23.10050 13.85700 1.710999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4140261E-02 2.6419206E-02 midg,1,midg; midg,igrid,midg -3.3357088E-02 1.3545635E-02 1,midg,midg; igrid,midg,midg -2.7262298E-02 1.6496431E-02 gauss-seidel spectral radius is 0.9986806 estimated iterations to convergence 218 setup time was (sec) 0.5400000 now iterating at: 06:30:50 rms-change max change #iterations 4.033467 176.9836 at 10iterations 1.910284 67.80129 at 20iterations 0.9017595 31.55276 at 30iterations 0.4288986 16.10145 at 40iterations 0.2031153 6.646974 at 50iterations 9.6291073E-02 3.200158 at 60iterations 4.5597900E-02 1.653469 at 70iterations 2.1612523E-02 0.7907791 at 80iterations 1.0239881E-02 0.3498745 at 90iterations 4.8773438E-03 0.1692004 at 100iterations 2.3098113E-03 7.0351601E-02 at 110iterations 1.0945143E-03 3.6678314E-02 at 120iterations finished qdiffx linear iterations at : 06:30:57 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.0945143E-03 3.6678314E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 06:30:57 7.663u 0.199s 0:08.13 96.5% 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 Sun Oct 9 2011 at 06:30:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 300 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.982574 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): 1.878000 44.32300 ymin,ymax (A): -9.236000 36.95000 zmin,zma (A): -25.14500 28.56700 x,y,z range (A): 42.44500 46.18600 53.71200 scale (grids/A): 2.982574 object centre (A): 23.10050 13.85700 1.710999 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -2.499985 assigned positive charge : 298.8980 centred at (gu) : 89.49512 87.69722 84.56382 assigned negative charge : -301.3981 centred at (gu) : 88.83707 86.92445 84.31121 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 145565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17438 grid for indexing accessible points = 1.400000 m= 74840 mr = 105007 m= 28457 mr = 61970 m= 7595 mr = 23510 m= 1453 mr = 6027 m= 170 mr = 1129 m= 7 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2008 time to turn everything in is 0.8200000 number of dielectric boundary points 60349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 14840 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) : 1.988383 object centre at (A) : 23.10050 13.85700 1.710999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5412860 0.8496862 midg,1,midg; midg,igrid,midg -0.2826179 0.1604993 1,midg,midg; igrid,midg,midg -0.2553309 0.1499876 gauss-seidel spectral radius is 0.9992536 estimated iterations to convergence 289 setup time was (sec) 1.050000 now iterating at: 06:30:59 rms-change max change #iterations 9.245619 486.6841 at 10iterations 5.319932 128.6333 at 20iterations 3.053344 67.59282 at 30iterations 1.752779 38.30765 at 40iterations 1.002533 20.04989 at 50iterations 0.5750263 10.45310 at 60iterations 0.3298638 6.492836 at 70iterations 0.1882527 3.821632 at 80iterations 0.1082387 2.254483 at 90iterations 6.1942659E-02 1.177849 at 100iterations 3.5417270E-02 0.7101705 at 110iterations 2.0234725E-02 0.3903687 at 120iterations 1.1596537E-02 0.2192879 at 130iterations 6.6464753E-03 0.1173859 at 140iterations 3.8099373E-03 7.1641922E-02 at 150iterations 2.1800508E-03 3.8531303E-02 at 160iterations 1.2460363E-03 2.3094177E-02 at 170iterations 7.1406458E-04 1.2962341E-02 at 180iterations finished qdiffx linear iterations at : 06:31:10 total time elapsed so far: 12.16000 # loops : 180 mean,max change (kT/e) : 7.1406458E-04 1.2962341E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 06:31:10 12.293u 0.226s 0:12.81 97.6% 0+0k 0+0io 0pf+0w