Sun Oct 9 08:14:32 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 Sun Oct 9 2011 at 08:14:32 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 !!! WARNING: NAP 1039 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5222161 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): -26.18100 22.94700 ymin,ymax (A): -23.61000 36.38200 zmin,zma (A): -18.03400 50.13700 x,y,z range (A): 49.12800 59.99200 68.17101 scale (grids/A): 0.5222161 object centre (A): -1.617000 6.386000 16.05150 number of atom coordinates read : 3671 total number of charged atoms : 3530 net assigned charge : 13.00004 assigned positive charge : 553.0261 centred at (gu) : 89.90486 87.95262 89.97021 assigned negative charge : -540.0277 centred at (gu) : 89.96686 87.88113 90.01201 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6489 nv = 96 ne = 84 npr = 72808 no. pairs analyzed = 72808 no. exposed pairs = 4925 no. arc points = 35613 no. surface atoms = 1605 nbur = 2066 mkacc time = 0.2000000 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 = 1.624000 m= 244 mr = 3139 m= 4 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3584 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3419 ## 470 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8613 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4510573E-10 1.7541830E-10 midg,1,midg; midg,igrid,midg 1.2694865E-10 3.1879871E-10 1,midg,midg; igrid,midg,midg 5.1731858E-10 1.0936408E-10 gauss-seidel spectral radius is 0.9811721 estimated iterations to convergence 60 setup time was (sec) 0.7000000 now iterating at: 08:14:33 rms-change max change #iterations 6.6365138E-02 10.52291 at 10iterations 4.1207699E-03 0.6054996 at 20iterations 5.7538948E-04 8.6160660E-02 at 30iterations 1.6595057E-04 2.3712158E-02 at 40iterations 5.2274212E-05 7.4622631E-03 at 50iterations finished qdiffx linear iterations at : 08:14:36 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 5.2274212E-05 7.4622631E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 08:14:37 4.175u 0.276s 0:04.72 94.0% 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 Sun Oct 9 2011 at 08:14:37 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 !!! WARNING: NAP 1039 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.566648 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): -26.18100 22.94700 ymin,ymax (A): -23.61000 36.38200 zmin,zma (A): -18.03400 50.13700 x,y,z range (A): 49.12800 59.99200 68.17101 scale (grids/A): 1.566648 object centre (A): -1.617000 6.386000 16.05150 number of atom coordinates read : 3671 total number of charged atoms : 3530 net assigned charge : 13.00004 assigned positive charge : 553.0261 centred at (gu) : 89.71349 83.85699 89.90959 assigned negative charge : -540.0277 centred at (gu) : 89.90027 83.64310 90.03593 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71844 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35613 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21735 mr = 47084 m= 2121 mr = 14333 m= 54 mr = 884 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 451 time to turn everything in is 0.6600000 number of dielectric boundary points 33453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 414 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 26695 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) : 0.5222161 object centre at (A) : -1.617000 6.386000 16.05150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9233787E-02 1.0132645E-02 midg,1,midg; midg,igrid,midg 4.9621053E-03 1.5985487E-02 1,midg,midg; igrid,midg,midg 1.0249632E-02 -8.1164838E-04 gauss-seidel spectral radius is 0.9981063 estimated iterations to convergence 183 setup time was (sec) 0.9500000 now iterating at: 08:14:38 rms-change max change #iterations 3.413179 161.3317 at 10iterations 1.393529 53.50363 at 20iterations 0.5705503 19.77877 at 30iterations 0.2328971 8.729443 at 40iterations 9.5634103E-02 3.923737 at 50iterations 3.9117914E-02 1.511644 at 60iterations 1.6102675E-02 0.5273743 at 70iterations 6.6243224E-03 0.2677388 at 80iterations 2.7513569E-03 9.7524107E-02 at 90iterations 1.1674184E-03 4.3795586E-02 at 100iterations 5.1470584E-04 1.7456055E-02 at 110iterations 2.4498109E-04 9.3278289E-03 at 120iterations finished qdiffx linear iterations at : 08:14:46 total time elapsed so far: 9.220000 # loops : 120 mean,max change (kT/e) : 2.4498109E-04 9.3278289E-03 energy calculations done at 9.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 08:14:47 9.386u 0.298s 0:09.97 96.9% 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 Sun Oct 9 2011 at 08:14:47 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3671 !!! WARNING: NAP 1039 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.349973 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): -26.18100 22.94700 ymin,ymax (A): -23.61000 36.38200 zmin,zma (A): -18.03400 50.13700 x,y,z range (A): 49.12800 59.99200 68.17101 scale (grids/A): 2.349973 object centre (A): -1.617000 6.386000 16.05150 number of atom coordinates read : 3671 total number of charged atoms : 3530 net assigned charge : 13.00004 assigned positive charge : 553.0261 centred at (gu) : 89.56982 80.78535 89.86435 assigned negative charge : -540.0277 centred at (gu) : 89.85028 80.46453 90.05372 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 166981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35613 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 75026 mr = 116172 m= 21124 mr = 57554 m= 3063 mr = 15383 m= 167 mr = 1751 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 1555 time to turn everything in is 1.590000 number of dielectric boundary points 75463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 28182 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) : 1.566648 object centre at (A) : -1.617000 6.386000 16.05150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2451238 0.1232767 midg,1,midg; midg,igrid,midg 0.1402267 0.3186995 1,midg,midg; igrid,midg,midg 0.1328871 -4.5490663E-02 gauss-seidel spectral radius is 0.9991362 estimated iterations to convergence 269 setup time was (sec) 1.920000 now iterating at: 08:14:49 rms-change max change #iterations 9.165734 306.4564 at 10iterations 5.196434 162.0983 at 20iterations 2.936962 73.22304 at 30iterations 1.647561 43.73421 at 40iterations 0.9178810 24.75105 at 50iterations 0.5114938 14.00831 at 60iterations 0.2830669 7.215116 at 70iterations 0.1570098 3.701614 at 80iterations 8.6676486E-02 2.112452 at 90iterations 4.7943473E-02 1.109917 at 100iterations 2.6410086E-02 0.6051912 at 110iterations 1.4544176E-02 0.3657417 at 120iterations 8.0219135E-03 0.1884346 at 130iterations 4.4118310E-03 0.1029015 at 140iterations 2.4269307E-03 5.7678223E-02 at 150iterations 1.3349847E-03 2.8211594E-02 at 160iterations 7.3392276E-04 1.7006159E-02 at 170iterations 4.0340496E-04 8.1062317E-03 at 180iterations finished qdiffx linear iterations at : 08:15:03 total time elapsed so far: 15.64000 # loops : 180 mean,max change (kT/e) : 4.0340496E-04 8.1062317E-03 energy calculations done at 15.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.81000 DelPhi exited at 08:15:03 15.808u 0.305s 0:16.38 98.2% 0+0k 0+0io 0pf+0w