Mon Oct 10 14:07:19 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 Mon Oct 10 2011 at 14:07:19 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5945025 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): 13.18700 65.05800 ymin,ymax (A): 2.108000 56.35500 zmin,zma (A): 86.02100 145.9030 x,y,z range (A): 51.87100 54.24700 59.88200 scale (grids/A): 0.5945025 object centre (A): 39.12250 29.23150 115.9620 number of atom coordinates read : 3048 total number of charged atoms : 2900 net assigned charge : -6.773973 assigned positive charge : 456.2016 centred at (gu) : 90.14509 92.04416 90.11960 assigned negative charge : -462.9768 centred at (gu) : 89.96754 91.92118 90.14722 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7086 nv = 96 ne = 84 npr = 62645 no. pairs analyzed = 62645 no. exposed pairs = 3714 no. arc points = 25991 no. surface atoms = 1247 nbur = 1801 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 325 mr = 3910 m= 0 mr = 21 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3600000 number of dielectric boundary points 3480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2688 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8991 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4711244E-09 -3.6222774E-09 midg,1,midg; midg,igrid,midg -4.4497694E-09 3.1911873E-09 1,midg,midg; igrid,midg,midg -8.8327914E-09 3.9715946E-09 gauss-seidel spectral radius is 0.9853939 estimated iterations to convergence 68 setup time was (sec) 0.6500000 now iterating at: 14:07:20 rms-change max change #iterations 0.1143916 19.07301 at 10iterations 1.0207413E-02 1.499531 at 20iterations 1.6330457E-03 0.3157845 at 30iterations 6.6521391E-04 0.1419239 at 40iterations 3.0119618E-04 6.4392090E-02 at 50iterations finished qdiffx linear iterations at : 14:07:24 total time elapsed so far: 4.580000 # loops : 50 mean,max change (kT/e) : 3.0119618E-04 6.4392090E-02 energy calculations done at 4.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.760000 DelPhi exited at 14:07:25 4.760u 0.401s 0:05.47 94.3% 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 Mon Oct 10 2011 at 14:07:25 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.783507 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): 13.18700 65.05800 ymin,ymax (A): 2.108000 56.35500 zmin,zma (A): 86.02100 145.9030 x,y,z range (A): 51.87100 54.24700 59.88200 scale (grids/A): 1.783507 object centre (A): 39.12250 29.23150 115.9620 number of atom coordinates read : 3048 total number of charged atoms : 2900 net assigned charge : -6.773973 assigned positive charge : 456.2016 centred at (gu) : 90.43447 96.13176 90.35816 assigned negative charge : -462.9768 centred at (gu) : 89.90231 95.76295 90.44138 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25991 grid for indexing accessible points = 1.400000 m= 25865 mr = 54536 m= 3229 mr = 18553 m= 128 mr = 1754 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1975 time to turn everything in is 0.6400000 number of dielectric boundary points 32206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22592 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) : 0.5945025 object centre at (A) : 39.12250 29.23150 115.9620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9879336E-02 -1.4972472E-02 midg,1,midg; midg,igrid,midg -3.8356576E-02 -2.2139391E-03 1,midg,midg; igrid,midg,midg -1.7998101E-02 3.8628920E-03 gauss-seidel spectral radius is 0.9984915 estimated iterations to convergence 204 setup time was (sec) 0.9400000 now iterating at: 14:07:26 rms-change max change #iterations 4.106241 156.9830 at 10iterations 1.841349 63.81159 at 20iterations 0.8354595 30.45240 at 30iterations 0.3757210 12.91740 at 40iterations 0.1691349 5.135719 at 50iterations 7.6645158E-02 2.403590 at 60iterations 3.4706991E-02 1.229207 at 70iterations 1.5947312E-02 0.5517178 at 80iterations 7.4903681E-03 0.2572379 at 90iterations 3.7957747E-03 0.1442490 at 100iterations 2.1540185E-03 8.9452744E-02 at 110iterations 1.3975987E-03 5.8666229E-02 at 120iterations finished qdiffx linear iterations at : 14:07:36 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 1.3975987E-03 5.8666229E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.05000 DelPhi exited at 14:07:37 11.059u 0.437s 0:12.11 94.7% 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 Mon Oct 10 2011 at 14:07:37 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: GLU 327 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.675261 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): 13.18700 65.05800 ymin,ymax (A): 2.108000 56.35500 zmin,zma (A): 86.02100 145.9030 x,y,z range (A): 51.87100 54.24700 59.88200 scale (grids/A): 2.675261 object centre (A): 39.12250 29.23150 115.9620 number of atom coordinates read : 3048 total number of charged atoms : 2900 net assigned charge : -6.773973 assigned positive charge : 456.2016 centred at (gu) : 90.65128 99.19738 90.53689 assigned negative charge : -462.9768 centred at (gu) : 89.85336 98.64444 90.66205 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 180714 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25991 grid for indexing accessible points = 1.400000 m= 87449 mr = 132769 m= 27473 mr = 70835 m= 5432 mr = 21257 m= 545 mr = 3750 m= 16 mr = 317 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 6464 time to turn everything in is 1.590000 number of dielectric boundary points 72702 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 23181 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) : 1.783507 object centre at (A) : 39.12250 29.23150 115.9620 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1964200 -0.1978394 midg,1,midg; midg,igrid,midg -0.5770373 -1.8174924E-02 1,midg,midg; igrid,midg,midg -8.5185021E-02 1.1063289E-03 gauss-seidel spectral radius is 0.9992286 estimated iterations to convergence 284 setup time was (sec) 1.920000 now iterating at: 14:07:40 rms-change max change #iterations 10.04758 286.6583 at 10iterations 5.829906 148.7252 at 20iterations 3.359829 82.27368 at 30iterations 1.931919 44.78627 at 40iterations 1.107193 23.28934 at 50iterations 0.6326295 12.25161 at 60iterations 0.3621525 7.328078 at 70iterations 0.2067907 4.398722 at 80iterations 0.1178786 2.240473 at 90iterations 6.7201957E-02 1.317704 at 100iterations 3.8394883E-02 0.7185974 at 110iterations 2.1894446E-02 0.4064674 at 120iterations 1.2550409E-02 0.2775517 at 130iterations 7.2625428E-03 0.1692762 at 140iterations 4.2840480E-03 9.1239929E-02 at 150iterations 2.6228738E-03 5.9177399E-02 at 160iterations 1.7082059E-03 3.9524078E-02 at 170iterations 1.2042605E-03 3.1909943E-02 at 180iterations finished qdiffx linear iterations at : 14:07:56 total time elapsed so far: 18.59000 # loops : 180 mean,max change (kT/e) : 1.2042605E-03 3.1909943E-02 energy calculations done at 18.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.75000 DelPhi exited at 14:07:57 18.752u 0.491s 0:19.66 97.8% 0+0k 0+0io 0pf+0w