Mon Oct 10 16:23:28 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 16:23:28 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 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: 0.5856418 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): 202.2130 254.5170 ymin,ymax (A): 62.16600 105.5920 zmin,zma (A): 157.6360 218.4240 x,y,z range (A): 52.30399 43.42600 60.78801 scale (grids/A): 0.5856418 object centre (A): 228.3650 83.87900 188.0300 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 10.50002 assigned positive charge : 352.5211 centred at (gu) : 90.49321 90.38605 89.86379 assigned negative charge : -342.0217 centred at (gu) : 90.61297 90.45803 89.91312 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5284 nv = 96 ne = 84 npr = 46350 no. pairs analyzed = 46350 no. exposed pairs = 3234 no. arc points = 23337 no. surface atoms = 1087 nbur = 1257 mkacc time = 9.9999994E-02 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 = 1.456000 m= 248 mr = 2474 m= 0 mr = 15 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2440 ## 334 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9281316E-09 1.7439525E-09 midg,1,midg; midg,igrid,midg 3.9038817E-09 1.4412105E-09 1,midg,midg; igrid,midg,midg 4.6578941E-09 3.5394720E-10 gauss-seidel spectral radius is 0.9849043 estimated iterations to convergence 67 setup time was (sec) 0.4900000 now iterating at: 16:23:29 rms-change max change #iterations 9.1134220E-02 17.45109 at 10iterations 7.3896837E-03 1.168350 at 20iterations 6.6046906E-04 0.1284466 at 30iterations 8.6955210E-05 2.1497726E-02 at 40iterations 1.8011317E-05 4.7988892E-03 at 50iterations finished qdiffx linear iterations at : 16:23:31 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 1.8011317E-05 4.7988892E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 16:23:32 3.238u 0.185s 0:03.70 92.1% 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 16:23:32 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.756925 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): 202.2130 254.5170 ymin,ymax (A): 62.16600 105.5920 zmin,zma (A): 157.6360 218.4240 x,y,z range (A): 52.30399 43.42600 60.78801 scale (grids/A): 1.756925 object centre (A): 228.3650 83.87900 188.0300 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 10.50002 assigned positive charge : 352.5211 centred at (gu) : 91.47939 91.15759 89.59118 assigned negative charge : -342.0217 centred at (gu) : 91.83871 91.37388 89.73940 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 56512 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23337 grid for indexing accessible points = 1.400000 m= 17145 mr = 34969 m= 2085 mr = 11511 m= 88 mr = 1085 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 28246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 17054 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) : 0.5856418 object centre at (A) : 228.3650 83.87900 188.0300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5259764E-03 1.9523121E-02 midg,1,midg; midg,igrid,midg 1.0221354E-02 9.1203582E-03 1,midg,midg; igrid,midg,midg 1.5560090E-02 6.2707230E-03 gauss-seidel spectral radius is 0.9983805 estimated iterations to convergence 197 setup time was (sec) 0.7100000 now iterating at: 16:23:33 rms-change max change #iterations 3.419708 182.7185 at 10iterations 1.488299 67.32732 at 20iterations 0.6489998 23.96599 at 30iterations 0.2833849 11.36945 at 40iterations 0.1236656 4.623352 at 50iterations 5.4000758E-02 2.071793 at 60iterations 2.3616422E-02 0.9309235 at 70iterations 1.0332208E-02 0.4106159 at 80iterations 4.5487401E-03 0.1860790 at 90iterations 1.9931251E-03 7.4356079E-02 at 100iterations 8.8540534E-04 3.5655975E-02 at 110iterations 3.9779471E-04 1.7381668E-02 at 120iterations finished qdiffx linear iterations at : 16:23:39 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 3.9779471E-04 1.7381668E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 16:23:40 7.225u 0.217s 0:07.72 96.2% 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 16:23:40 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2344 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: 2.635388 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): 202.2130 254.5170 ymin,ymax (A): 62.16600 105.5920 zmin,zma (A): 157.6360 218.4240 x,y,z range (A): 52.30399 43.42600 60.78801 scale (grids/A): 2.635388 object centre (A): 228.3650 83.87900 188.0300 number of atom coordinates read : 2344 total number of charged atoms : 2206 net assigned charge : 10.50002 assigned positive charge : 352.5211 centred at (gu) : 92.21899 91.73632 89.38663 assigned negative charge : -342.0217 centred at (gu) : 92.75801 92.06083 89.60908 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 130327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23337 grid for indexing accessible points = 1.400000 m= 57919 mr = 86072 m= 17828 mr = 44321 m= 3421 mr = 13303 m= 375 mr = 2315 m= 12 mr = 219 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9800000 number of dielectric boundary points 63652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17622 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) : 1.756925 object centre at (A) : 228.3650 83.87900 188.0300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5641611 0.2464487 midg,1,midg; midg,igrid,midg 8.7450758E-02 0.1073277 1,midg,midg; igrid,midg,midg 0.1497541 7.1580850E-02 gauss-seidel spectral radius is 0.9991898 estimated iterations to convergence 277 setup time was (sec) 1.290000 now iterating at: 16:23:41 rms-change max change #iterations 8.425639 272.3310 at 10iterations 4.796790 147.5293 at 20iterations 2.715224 67.15726 at 30iterations 1.525329 36.66430 at 40iterations 0.8589423 18.73050 at 50iterations 0.4800847 10.23274 at 60iterations 0.2686474 5.758952 at 70iterations 0.1502367 3.400617 at 80iterations 8.3971307E-02 1.761503 at 90iterations 4.6921041E-02 0.9740601 at 100iterations 2.6204057E-02 0.5840797 at 110iterations 1.4625079E-02 0.3367844 at 120iterations 8.1792409E-03 0.1825886 at 130iterations 4.5711105E-03 9.2842102E-02 at 140iterations 2.5629147E-03 5.8647156E-02 at 150iterations 1.4391959E-03 3.5797119E-02 at 160iterations 8.1105891E-04 1.7021179E-02 at 170iterations 4.6124368E-04 1.0073543E-02 at 180iterations finished qdiffx linear iterations at : 16:23:51 total time elapsed so far: 11.31000 # loops : 180 mean,max change (kT/e) : 4.6124368E-04 1.0073543E-02 energy calculations done at 11.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 16:23:52 11.498u 0.225s 0:12.00 97.5% 0+0k 0+0io 0pf+0w