Sat Oct 8 19:30:18 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 Sat Oct 8 2011 at 19:30:18 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 935 has a net charge of 1.4000 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: 0.6313512 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): -10.31200 38.76300 ymin,ymax (A): -22.08100 24.88700 zmin,zma (A): -12.30600 44.08100 x,y,z range (A): 49.07500 46.96800 56.38700 scale (grids/A): 0.6313512 object centre (A): 14.22550 1.403000 15.88750 number of atom coordinates read : 2593 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 88.42377 89.21923 89.84540 assigned negative charge : -387.4045 centred at (gu) : 88.30515 89.26627 89.75053 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6651 nv = 96 ne = 84 npr = 55368 no. pairs analyzed = 55368 no. exposed pairs = 2943 no. arc points = 20858 no. surface atoms = 989 nbur = 1604 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 305 mr = 3731 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.2000000 number of dielectric boundary points 3187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8220 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2159067E-09 1.2837065E-08 midg,1,midg; midg,igrid,midg 1.0619827E-08 3.5019099E-10 1,midg,midg; igrid,midg,midg -9.0632151E-09 1.0963841E-08 gauss-seidel spectral radius is 0.9869965 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 19:30:18 rms-change max change #iterations 0.1384156 19.86668 at 10iterations 1.3126059E-02 1.884018 at 20iterations 1.2721714E-03 0.1948862 at 30iterations 1.2247947E-04 1.8272400E-02 at 40iterations 1.1852208E-05 1.8024445E-03 at 50iterations finished qdiffx linear iterations at : 19:30:21 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1852208E-05 1.8024445E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 19:30:22 3.345u 0.173s 0:03.78 92.8% 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 19:30:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 935 has a net charge of 1.4000 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: 1.894054 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): -10.31200 38.76300 ymin,ymax (A): -22.08100 24.88700 zmin,zma (A): -12.30600 44.08100 x,y,z range (A): 49.07500 46.96800 56.38700 scale (grids/A): 1.894054 object centre (A): 14.22550 1.403000 15.88750 number of atom coordinates read : 2593 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 85.27055 87.65749 89.53573 assigned negative charge : -387.4045 centred at (gu) : 84.91513 87.79861 89.25148 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20858 grid for indexing accessible points = 1.400000 m= 24948 mr = 51183 m= 3566 mr = 18456 m= 173 mr = 2203 m= 0 mr = 69 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4520 time to turn everything in is 0.3600000 number of dielectric boundary points 29359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19316 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) : 0.6313512 object centre at (A) : 14.22550 1.403000 15.88750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8668696E-02 2.3459077E-02 midg,1,midg; midg,igrid,midg 1.7980788E-02 2.3462684E-03 1,midg,midg; igrid,midg,midg -5.6512370E-03 4.0755440E-02 gauss-seidel spectral radius is 0.9986117 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 19:30:23 rms-change max change #iterations 4.167655 176.3181 at 10iterations 1.932658 63.89021 at 20iterations 0.9043241 28.03495 at 30iterations 0.4196223 14.32331 at 40iterations 0.1959047 6.831108 at 50iterations 9.1183394E-02 3.223953 at 60iterations 4.2563520E-02 1.366096 at 70iterations 1.9774435E-02 0.6231670 at 80iterations 9.1993492E-03 0.2833233 at 90iterations 4.2794519E-03 0.1281452 at 100iterations 1.9931176E-03 5.9753418E-02 at 110iterations 9.3016500E-04 2.7686119E-02 at 120iterations finished qdiffx linear iterations at : 19:30:30 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 9.3016500E-04 2.7686119E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 19:30:30 7.755u 0.187s 0:08.21 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 Sat Oct 8 2011 at 19:30:30 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN9 935 has a net charge of 1.4000 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: 2.841080 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): -10.31200 38.76300 ymin,ymax (A): -22.08100 24.88700 zmin,zma (A): -12.30600 44.08100 x,y,z range (A): 49.07500 46.96800 56.38700 scale (grids/A): 2.841080 object centre (A): 14.22550 1.403000 15.88750 number of atom coordinates read : 2593 total number of charged atoms : 2454 net assigned charge : 4.000009 assigned positive charge : 391.4040 centred at (gu) : 82.90572 86.48603 89.30360 assigned negative charge : -387.4045 centred at (gu) : 82.37260 86.69791 88.87727 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20858 grid for indexing accessible points = 1.400000 m= 83083 mr = 123759 m= 27715 mr = 68497 m= 6215 mr = 22220 m= 742 mr = 4630 m= 43 mr = 525 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 15262 time to turn everything in is 0.8900000 number of dielectric boundary points 66292 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19630 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) : 1.894054 object centre at (A) : 14.22550 1.403000 15.88750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1332566 0.3168494 midg,1,midg; midg,igrid,midg 0.1905642 2.1289658E-02 1,midg,midg; igrid,midg,midg -3.0872103E-02 0.5303113 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.110000 now iterating at: 19:30:31 rms-change max change #iterations 9.661223 342.2070 at 10iterations 5.561758 126.4170 at 20iterations 3.183550 69.71469 at 30iterations 1.822113 36.34842 at 40iterations 1.041767 19.98551 at 50iterations 0.5939991 11.71057 at 60iterations 0.3404393 6.534815 at 70iterations 0.1947491 3.481924 at 80iterations 0.1110169 2.204128 at 90iterations 6.3489668E-02 1.206350 at 100iterations 3.6260698E-02 0.6171083 at 110iterations 2.0678004E-02 0.3735476 at 120iterations 1.1815292E-02 0.2185421 at 130iterations 6.7373221E-03 0.1216908 at 140iterations 3.8468870E-03 6.8069458E-02 at 150iterations 2.1943788E-03 4.0544033E-02 at 160iterations 1.2550112E-03 2.4085999E-02 at 170iterations 7.1622862E-04 1.2544632E-02 at 180iterations finished qdiffx linear iterations at : 19:30:43 total time elapsed so far: 12.32000 # loops : 180 mean,max change (kT/e) : 7.1622862E-04 1.2544632E-02 energy calculations done at 12.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 19:30:43 12.453u 0.209s 0:12.92 97.9% 0+0k 0+0io 0pf+0w