Sat Oct 8 11:37:31 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 Sat Oct 8 2011 at 11:37:31 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 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: 0.6252305 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): 16.81000 70.19300 ymin,ymax (A): 10.21000 67.14900 zmin,zma (A): -7.214000 38.40400 x,y,z range (A): 53.38300 56.93900 45.61800 scale (grids/A): 0.6252305 object centre (A): 43.50150 38.67950 15.59500 number of atom coordinates read : 2387 total number of charged atoms : 2239 net assigned charge : -1.999994 assigned positive charge : 346.8120 centred at (gu) : 88.97086 90.76270 89.66899 assigned negative charge : -348.8124 centred at (gu) : 88.93480 90.75269 89.62604 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6260 nv = 96 ne = 84 npr = 48405 no. pairs analyzed = 48405 no. exposed pairs = 3127 no. arc points = 21951 no. surface atoms = 1049 nbur = 1338 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 3248 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2116 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7544 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2053686E-09 1.0294993E-09 midg,1,midg; midg,igrid,midg -2.1620121E-09 -1.3504927E-09 1,midg,midg; igrid,midg,midg -5.4632374E-09 4.9307497E-10 gauss-seidel spectral radius is 0.9867392 estimated iterations to convergence 71 setup time was (sec) 0.3700000 now iterating at: 11:37:32 rms-change max change #iterations 0.1272503 22.48074 at 10iterations 1.1756868E-02 1.775130 at 20iterations 1.1001508E-03 0.1810455 at 30iterations 1.0623860E-04 2.1109581E-02 at 40iterations 1.0715017E-05 1.4648438E-03 at 50iterations finished qdiffx linear iterations at : 11:37:35 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0715017E-05 1.4648438E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 11:37:35 3.352u 0.194s 0:04.40 80.4% 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 Sat Oct 8 2011 at 11:37:36 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 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: 1.875691 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): 16.81000 70.19300 ymin,ymax (A): 10.21000 67.14900 zmin,zma (A): -7.214000 38.40400 x,y,z range (A): 53.38300 56.93900 45.61800 scale (grids/A): 1.875691 object centre (A): 43.50150 38.67950 15.59500 number of atom coordinates read : 2387 total number of charged atoms : 2239 net assigned charge : -1.999994 assigned positive charge : 346.8120 centred at (gu) : 86.91215 92.28769 89.00636 assigned negative charge : -348.8124 centred at (gu) : 86.80418 92.25771 88.87781 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21951 grid for indexing accessible points = 1.400000 m= 23010 mr = 45042 m= 3188 mr = 16509 m= 138 mr = 1741 m= 4 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.3300000 number of dielectric boundary points 30499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17599 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) : 0.6252305 object centre at (A) : 43.50150 38.67950 15.59500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.7242117E-03 1.3730287E-03 midg,1,midg; midg,igrid,midg 1.2104372E-02 1.5567780E-03 1,midg,midg; igrid,midg,midg -2.2890745E-02 -2.2877542E-02 gauss-seidel spectral radius is 0.9985781 estimated iterations to convergence 210 setup time was (sec) 0.5500000 now iterating at: 11:37:36 rms-change max change #iterations 3.915867 199.1794 at 10iterations 1.795376 67.07538 at 20iterations 0.8279577 26.37025 at 30iterations 0.3802330 14.04957 at 40iterations 0.1753522 6.080178 at 50iterations 8.0726482E-02 2.633479 at 60iterations 3.7205711E-02 1.398193 at 70iterations 1.7127572E-02 0.5288004 at 80iterations 7.8855148E-03 0.2458372 at 90iterations 3.6634719E-03 0.1336489 at 100iterations 1.6833709E-03 6.3771725E-02 at 110iterations 7.7852613E-04 2.6209831E-02 at 120iterations finished qdiffx linear iterations at : 11:37:43 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 7.7852613E-04 2.6209831E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 11:37:44 7.694u 0.200s 0:08.90 88.6% 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 Sat Oct 8 2011 at 11:37:45 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2387 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: 2.813537 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): 16.81000 70.19300 ymin,ymax (A): 10.21000 67.14900 zmin,zma (A): -7.214000 38.40400 x,y,z range (A): 53.38300 56.93900 45.61800 scale (grids/A): 2.813537 object centre (A): 43.50150 38.67950 15.59500 number of atom coordinates read : 2387 total number of charged atoms : 2239 net assigned charge : -1.999994 assigned positive charge : 346.8120 centred at (gu) : 85.36808 93.43135 88.50950 assigned negative charge : -348.8124 centred at (gu) : 85.20628 93.38652 88.31671 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21951 grid for indexing accessible points = 1.400000 m= 74789 mr = 109714 m= 26019 mr = 59932 m= 5455 mr = 20555 m= 630 mr = 3801 m= 33 mr = 329 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 534 time to turn everything in is 0.8400000 number of dielectric boundary points 68783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 17908 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) : 1.875691 object centre at (A) : 43.50150 38.67950 15.59500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1373134 1.0561791E-02 midg,1,midg; midg,igrid,midg 0.2432472 2.1955350E-02 1,midg,midg; igrid,midg,midg -0.2605529 -0.2238778 gauss-seidel spectral radius is 0.9992472 estimated iterations to convergence 288 setup time was (sec) 1.070000 now iterating at: 11:37:46 rms-change max change #iterations 9.253006 372.0420 at 10iterations 5.409184 149.2468 at 20iterations 3.130957 74.41245 at 30iterations 1.804978 44.90368 at 40iterations 1.038366 22.63512 at 50iterations 0.5987226 13.42982 at 60iterations 0.3434725 7.492655 at 70iterations 0.1970835 3.919689 at 80iterations 0.1131170 2.206849 at 90iterations 6.4767808E-02 1.322494 at 100iterations 3.7038490E-02 0.7729053 at 110iterations 2.1240711E-02 0.4321594 at 120iterations 1.2159057E-02 0.2394037 at 130iterations 6.9686710E-03 0.1744289 at 140iterations 3.9960723E-03 8.9023590E-02 at 150iterations 2.2930559E-03 4.7123551E-02 at 160iterations 1.3247860E-03 2.6979923E-02 at 170iterations 7.6868659E-04 1.5786171E-02 at 180iterations finished qdiffx linear iterations at : 11:37:57 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 7.6868659E-04 1.5786171E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 11:37:57 12.370u 0.223s 0:12.91 97.5% 0+0k 0+0io 0pf+0w