Sat Oct 8 14:50:56 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 Sat Oct 8 2011 at 14:50:56 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6398044 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): -12.23500 43.40700 ymin,ymax (A): -23.96800 22.95500 zmin,zma (A): -7.602000 47.60400 x,y,z range (A): 55.64200 46.92300 55.20600 scale (grids/A): 0.6398044 object centre (A): 15.58600 -0.5065002 20.00100 number of atom coordinates read : 3002 total number of charged atoms : 2857 net assigned charge : 1.742007 assigned positive charge : 450.7066 centred at (gu) : 88.80532 89.99728 91.71144 assigned negative charge : -448.9654 centred at (gu) : 88.73685 89.84236 91.70583 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8096 nv = 96 ne = 84 npr = 62718 no. pairs analyzed = 62718 no. exposed pairs = 3395 no. arc points = 23986 no. surface atoms = 1159 nbur = 1843 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4702 m= 0 mr = 46 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3401957E-09 4.8705298E-09 midg,1,midg; midg,igrid,midg -1.8420154E-08 2.2975382E-08 1,midg,midg; igrid,midg,midg -8.6001144E-09 9.0733527E-09 gauss-seidel spectral radius is 0.9873745 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:50:57 rms-change max change #iterations 0.1623337 19.85215 at 10iterations 1.6072918E-02 2.314795 at 20iterations 1.6657686E-03 0.2136154 at 30iterations 1.9861640E-04 2.6584625E-02 at 40iterations 2.7789740E-05 4.1732788E-03 at 50iterations finished qdiffx linear iterations at : 14:51:01 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 2.7789740E-05 4.1732788E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 14:51:02 4.520u 0.418s 0:05.27 93.5% 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 14:51:02 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.919413 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): -12.23500 43.40700 ymin,ymax (A): -23.96800 22.95500 zmin,zma (A): -7.602000 47.60400 x,y,z range (A): 55.64200 46.92300 55.20600 scale (grids/A): 1.919413 object centre (A): 15.58600 -0.5065002 20.00100 number of atom coordinates read : 3002 total number of charged atoms : 2857 net assigned charge : 1.742007 assigned positive charge : 450.7066 centred at (gu) : 86.41535 89.99136 95.13378 assigned negative charge : -448.9654 centred at (gu) : 86.21045 89.52672 95.11715 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23986 grid for indexing accessible points = 1.400000 m= 31887 mr = 64123 m= 4773 mr = 23950 m= 296 mr = 2896 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.7100000 number of dielectric boundary points 34780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22519 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) : 0.6398044 object centre at (A) : 15.58600 -0.5065002 20.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3630705E-02 1.0392220E-02 midg,1,midg; midg,igrid,midg -2.3656865E-03 3.3590764E-02 1,midg,midg; igrid,midg,midg -2.8471487E-02 1.1521528E-02 gauss-seidel spectral radius is 0.9986890 estimated iterations to convergence 219 setup time was (sec) 1.060000 now iterating at: 14:51:03 rms-change max change #iterations 4.701318 178.8437 at 10iterations 2.243243 65.91879 at 20iterations 1.067225 33.81655 at 30iterations 0.5079764 15.32398 at 40iterations 0.2414599 7.018697 at 50iterations 0.1153484 3.494044 at 60iterations 5.5001922E-02 1.691437 at 70iterations 2.6136497E-02 0.7835445 at 80iterations 1.2488691E-02 0.3682556 at 90iterations 5.9305108E-03 0.1724377 at 100iterations 2.8222019E-03 8.2504272E-02 at 110iterations 1.3515021E-03 3.8439989E-02 at 120iterations finished qdiffx linear iterations at : 14:51:13 total time elapsed so far: 10.62000 # loops : 120 mean,max change (kT/e) : 1.3515021E-03 3.8439989E-02 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 14:51:13 10.792u 0.437s 0:11.57 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 Sat Oct 8 2011 at 14:51:13 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.879120 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): -12.23500 43.40700 ymin,ymax (A): -23.96800 22.95500 zmin,zma (A): -7.602000 47.60400 x,y,z range (A): 55.64200 46.92300 55.20600 scale (grids/A): 2.879120 object centre (A): 15.58600 -0.5065002 20.00100 number of atom coordinates read : 3002 total number of charged atoms : 2857 net assigned charge : 1.742007 assigned positive charge : 450.7066 centred at (gu) : 84.62286 89.98676 97.70053 assigned negative charge : -448.9654 centred at (gu) : 84.31570 89.28991 97.67557 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 205858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23986 grid for indexing accessible points = 1.400000 m= 104635 mr = 154591 m= 36385 mr = 87219 m= 8338 mr = 29287 m= 1219 mr = 6181 m= 74 mr = 849 m= 0 mr = 35 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 1.850000 number of dielectric boundary points 78347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 22856 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) : 1.919413 object centre at (A) : 15.58600 -0.5065002 20.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0006101E-02 0.2602179 midg,1,midg; midg,igrid,midg -2.5600165E-02 0.3601181 1,midg,midg; igrid,midg,midg -0.2932603 0.1747427 gauss-seidel spectral radius is 0.9992782 estimated iterations to convergence 294 setup time was (sec) 2.180000 now iterating at: 14:51:16 rms-change max change #iterations 10.91099 485.3988 at 10iterations 6.387647 139.9161 at 20iterations 3.725321 69.13466 at 30iterations 2.169017 40.74034 at 40iterations 1.257512 24.78502 at 50iterations 0.7312074 12.01673 at 60iterations 0.4237212 7.088997 at 70iterations 0.2457457 4.286805 at 80iterations 0.1423401 2.410923 at 90iterations 8.2526490E-02 1.455414 at 100iterations 4.7756538E-02 0.7865610 at 110iterations 2.7672881E-02 0.4684502 at 120iterations 1.6023334E-02 0.2574234 at 130iterations 9.2877895E-03 0.1508904 at 140iterations 5.3805648E-03 8.6714745E-02 at 150iterations 3.1239274E-03 5.6083679E-02 at 160iterations 1.8187198E-03 3.0770302E-02 at 170iterations 1.0633236E-03 1.9138336E-02 at 180iterations finished qdiffx linear iterations at : 14:51:33 total time elapsed so far: 19.00000 # loops : 180 mean,max change (kT/e) : 1.0633236E-03 1.9138336E-02 energy calculations done at 19.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.17000 DelPhi exited at 14:51:33 19.178u 0.480s 0:19.98 98.3% 0+0k 0+0io 0pf+0w