Sun Oct 9 16:03:27 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 Sun Oct 9 2011 at 16:03:27 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6292977 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): -15.16500 37.71900 ymin,ymax (A): 56.04000 107.8380 zmin,zma (A): -4.934000 51.63700 x,y,z range (A): 52.88400 51.79800 56.57100 scale (grids/A): 0.6292977 object centre (A): 11.27700 81.93900 23.35150 number of atom coordinates read : 3189 total number of charged atoms : 3044 net assigned charge : -2.499986 assigned positive charge : 476.1739 centred at (gu) : 89.68830 88.47083 91.08288 assigned negative charge : -478.6754 centred at (gu) : 89.74111 88.37044 91.15705 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8227 nv = 96 ne = 84 npr = 66299 no. pairs analyzed = 66299 no. exposed pairs = 3716 no. arc points = 26146 no. surface atoms = 1263 nbur = 1926 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4598 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2613 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10246 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.2694501E-09 -1.3133873E-08 midg,1,midg; midg,igrid,midg -1.8513958E-08 5.8225895E-09 1,midg,midg; igrid,midg,midg 3.4484113E-09 -7.5142328E-09 gauss-seidel spectral radius is 0.9869670 estimated iterations to convergence 72 setup time was (sec) 0.5600000 now iterating at: 16:03:27 rms-change max change #iterations 0.1535962 19.83432 at 10iterations 1.5076961E-02 2.123528 at 20iterations 1.7646721E-03 0.2884064 at 30iterations 3.3729867E-04 6.0184479E-02 at 40iterations 9.5172356E-05 1.7597198E-02 at 50iterations finished qdiffx linear iterations at : 16:03:30 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 9.5172356E-05 1.7597198E-02 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.180000 DelPhi exited at 16:03:31 3.189u 0.146s 0:03.93 84.4% 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 Sun Oct 9 2011 at 16:03:31 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.887893 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): -15.16500 37.71900 ymin,ymax (A): 56.04000 107.8380 zmin,zma (A): -4.934000 51.63700 x,y,z range (A): 52.88400 51.79800 56.57100 scale (grids/A): 1.887893 object centre (A): 11.27700 81.93900 23.35150 number of atom coordinates read : 3189 total number of charged atoms : 3044 net assigned charge : -2.499986 assigned positive charge : 476.1739 centred at (gu) : 89.06394 85.41174 93.24792 assigned negative charge : -478.6754 centred at (gu) : 89.22330 85.11096 93.47098 start vw surface at 0.2200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 89685 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26146 grid for indexing accessible points = 1.400000 m= 32413 mr = 63379 m= 5661 mr = 23905 m= 381 mr = 3737 m= 4 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 665 time to turn everything in is 0.6600000 number of dielectric boundary points 36973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23889 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) : 0.6292977 object centre at (A) : 11.27700 81.93900 23.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9685434E-02 8.6785480E-03 midg,1,midg; midg,igrid,midg -2.4439478E-02 -4.9747629E-03 1,midg,midg; igrid,midg,midg -2.9188832E-02 -2.8446864E-02 gauss-seidel spectral radius is 0.9986576 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 16:03:32 rms-change max change #iterations 4.736495 221.0661 at 10iterations 2.225003 65.34588 at 20iterations 1.048616 33.65872 at 30iterations 0.4947559 17.27932 at 40iterations 0.2340810 8.277855 at 50iterations 0.1101366 3.222153 at 60iterations 5.2216411E-02 1.409365 at 70iterations 2.4662958E-02 0.7707834 at 80iterations 1.1698530E-02 0.3643179 at 90iterations 5.5696256E-03 0.1748552 at 100iterations 2.6841920E-03 7.8205109E-02 at 110iterations 1.3058407E-03 3.8757324E-02 at 120iterations finished qdiffx linear iterations at : 16:03:38 total time elapsed so far: 7.110000 # loops : 120 mean,max change (kT/e) : 1.3058407E-03 3.8757324E-02 energy calculations done at 7.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 16:03:39 7.292u 0.170s 0:07.74 96.3% 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 Sun Oct 9 2011 at 16:03:39 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3189 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.831840 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): -15.16500 37.71900 ymin,ymax (A): 56.04000 107.8380 zmin,zma (A): -4.934000 51.63700 x,y,z range (A): 52.88400 51.79800 56.57100 scale (grids/A): 2.831840 object centre (A): 11.27700 81.93900 23.35150 number of atom coordinates read : 3189 total number of charged atoms : 3044 net assigned charge : -2.499986 assigned positive charge : 476.1739 centred at (gu) : 88.59574 83.11749 94.87163 assigned negative charge : -478.6754 centred at (gu) : 88.83491 82.66631 95.20644 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 207637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26146 grid for indexing accessible points = 1.400000 m= 104352 mr = 153779 m= 39213 mr = 85439 m= 10474 mr = 31554 m= 1732 mr = 8150 m= 124 mr = 1246 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 2071 time to turn everything in is 1.560000 number of dielectric boundary points 83307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 24350 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) : 1.887893 object centre at (A) : 11.27700 81.93900 23.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5327917 0.2213001 midg,1,midg; midg,igrid,midg -0.2738429 -0.2019922 1,midg,midg; igrid,midg,midg -0.3737116 -0.3172077 gauss-seidel spectral radius is 0.9992749 estimated iterations to convergence 293 setup time was (sec) 1.840000 now iterating at: 16:03:41 rms-change max change #iterations 11.11679 298.3337 at 10iterations 6.559406 130.2563 at 20iterations 3.843910 75.74772 at 30iterations 2.253733 37.64051 at 40iterations 1.313313 23.80787 at 50iterations 0.7643651 14.45959 at 60iterations 0.4447028 8.854662 at 70iterations 0.2581292 4.279095 at 80iterations 0.1501441 2.547729 at 90iterations 8.7007150E-02 1.448051 at 100iterations 5.0454203E-02 0.8870564 at 110iterations 2.9317338E-02 0.4989643 at 120iterations 1.7025342E-02 0.2700951 at 130iterations 9.9363541E-03 0.1716039 at 140iterations 5.7976469E-03 9.5085144E-02 at 150iterations 3.4249695E-03 6.3552856E-02 at 160iterations 2.0527844E-03 3.6594391E-02 at 170iterations 1.2615026E-03 2.4803162E-02 at 180iterations finished qdiffx linear iterations at : 16:03:50 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 1.2615026E-03 2.4803162E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 16:03:51 11.867u 0.204s 0:12.34 97.7% 0+0k 0+0io 0pf+0w