Tue Oct 11 08:37:56 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 Tue Oct 11 2011 at 08:37:57 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2068 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7065595 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): 19.00600 64.42600 ymin,ymax (A): -3.438000 33.50500 zmin,zma (A): 20.24200 70.62700 x,y,z range (A): 45.42000 36.94300 50.38500 scale (grids/A): 0.7065595 object centre (A): 41.71600 15.03350 45.43450 number of atom coordinates read : 2068 total number of charged atoms : 1934 net assigned charge : 5.945010 assigned positive charge : 315.7281 centred at (gu) : 89.88570 89.71933 89.66676 assigned negative charge : -309.7831 centred at (gu) : 90.03546 89.75021 89.63019 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7033 nv = 96 ne = 84 npr = 41800 no. pairs analyzed = 41800 no. exposed pairs = 2511 no. arc points = 17164 no. surface atoms = 850 nbur = 1218 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 469 mr = 4085 m= 4 mr = 102 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1601 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7801 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3408611E-08 6.2566407E-08 midg,1,midg; midg,igrid,midg 6.7473287E-08 3.2500459E-08 1,midg,midg; igrid,midg,midg 1.2289166E-07 -2.3480267E-08 gauss-seidel spectral radius is 0.9895572 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 08:37:58 rms-change max change #iterations 0.2020556 32.16623 at 10iterations 2.4821466E-02 4.001827 at 20iterations 3.1854340E-03 0.4220114 at 30iterations 4.9295998E-04 6.5608978E-02 at 40iterations 1.0399509E-04 1.2729645E-02 at 50iterations finished qdiffx linear iterations at : 08:38:01 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 1.0399509E-04 1.2729645E-02 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 08:38:01 4.020u 0.164s 0:04.52 92.4% 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 Tue Oct 11 2011 at 08:38:01 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2068 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.119678 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): 19.00600 64.42600 ymin,ymax (A): -3.438000 33.50500 zmin,zma (A): 20.24200 70.62700 x,y,z range (A): 45.42000 36.94300 50.38500 scale (grids/A): 2.119678 object centre (A): 41.71600 15.03350 45.43450 number of atom coordinates read : 2068 total number of charged atoms : 1934 net assigned charge : 5.945010 assigned positive charge : 315.7281 centred at (gu) : 89.65706 89.15793 89.00031 assigned negative charge : -309.7831 centred at (gu) : 90.10645 89.25066 88.89058 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 74457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17164 grid for indexing accessible points = 1.400000 m= 30526 mr = 53197 m= 6020 mr = 23352 m= 580 mr = 4047 m= 13 mr = 335 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 30665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 15367 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) : 0.7065595 object centre at (A) : 41.71600 15.03350 45.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1110836E-02 3.9968338E-02 midg,1,midg; midg,igrid,midg 2.7851975E-02 8.2159191E-03 1,midg,midg; igrid,midg,midg 3.5625376E-02 1.6930660E-02 gauss-seidel spectral radius is 0.9988266 estimated iterations to convergence 231 setup time was (sec) 1.050000 now iterating at: 08:38:03 rms-change max change #iterations 4.608115 195.2401 at 10iterations 2.283548 76.10914 at 20iterations 1.129573 39.29074 at 30iterations 0.5610898 16.54107 at 40iterations 0.2781959 8.353140 at 50iterations 0.1383297 4.006359 at 60iterations 6.8620145E-02 2.163124 at 70iterations 3.4136098E-02 1.004787 at 80iterations 1.6979055E-02 0.5548792 at 90iterations 8.5318564E-03 0.2995300 at 100iterations 4.2853500E-03 0.1286068 at 110iterations 2.1856118E-03 6.3255310E-02 at 120iterations finished qdiffx linear iterations at : 08:38:10 total time elapsed so far: 8.700000 # loops : 120 mean,max change (kT/e) : 2.1856118E-03 6.3255310E-02 energy calculations done at 8.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.940000 DelPhi exited at 08:38:11 8.942u 0.174s 0:09.40 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 Tue Oct 11 2011 at 08:38:11 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2068 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.179518 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): 19.00600 64.42600 ymin,ymax (A): -3.438000 33.50500 zmin,zma (A): 20.24200 70.62700 x,y,z range (A): 45.42000 36.94300 50.38500 scale (grids/A): 3.179518 object centre (A): 41.71600 15.03350 45.43450 number of atom coordinates read : 2068 total number of charged atoms : 1934 net assigned charge : 5.945010 assigned positive charge : 315.7281 centred at (gu) : 89.48578 88.73684 88.50054 assigned negative charge : -309.7831 centred at (gu) : 90.15974 88.87595 88.33585 start vw surface at 0.1800000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 171408 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17164 grid for indexing accessible points = 1.400000 m= 94614 mr = 127407 m= 39091 mr = 79345 m= 11434 mr = 32454 m= 2422 mr = 8820 m= 287 mr = 1877 m= 2 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.240000 number of dielectric boundary points 69158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.400000 number of grid points assigned charge 15472 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) : 2.119678 object centre at (A) : 41.71600 15.03350 45.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2314596 0.3290617 midg,1,midg; midg,igrid,midg 0.2167427 6.1957441E-02 1,midg,midg; igrid,midg,midg 0.2986214 0.3229333 gauss-seidel spectral radius is 0.9992922 estimated iterations to convergence 297 setup time was (sec) 2.600000 now iterating at: 08:38:14 rms-change max change #iterations 10.25227 388.0236 at 10iterations 6.033668 117.9555 at 20iterations 3.552184 66.69792 at 30iterations 2.089213 39.26043 at 40iterations 1.225840 21.67401 at 50iterations 0.7169065 14.71548 at 60iterations 0.4200835 7.753334 at 70iterations 0.2454347 4.047681 at 80iterations 0.1438365 2.586458 at 90iterations 8.4065400E-02 1.493850 at 100iterations 4.9167920E-02 0.8978386 at 110iterations 2.8929723E-02 0.4986229 at 120iterations 1.7104803E-02 0.3197746 at 130iterations 1.0236799E-02 0.1865616 at 140iterations 6.2514301E-03 0.1169434 at 150iterations 3.9389851E-03 6.8782806E-02 at 160iterations 2.6030038E-03 4.9942017E-02 at 170iterations 1.8189379E-03 3.7929535E-02 at 180iterations finished qdiffx linear iterations at : 08:38:26 total time elapsed so far: 14.85000 # loops : 180 mean,max change (kT/e) : 1.8189379E-03 3.7929535E-02 energy calculations done at 14.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 08:38:26 15.077u 0.182s 0:15.57 97.9% 0+0k 0+0io 0pf+0w