Mon Oct 10 14:01:56 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 Mon Oct 10 2011 at 14:01:56 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 0.6750735 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): -14.33400 38.40100 ymin,ymax (A): 0.3790001 44.61300 zmin,zma (A): -7.211000 43.79800 x,y,z range (A): 52.73500 44.23400 51.00900 scale (grids/A): 0.6750735 object centre (A): 12.03350 22.49600 18.29350 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 373.0131 centred at (gu) : 90.55989 91.04258 90.22398 assigned negative charge : -369.5135 centred at (gu) : 90.75029 91.11405 90.18682 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7194 nv = 96 ne = 84 npr = 48426 no. pairs analyzed = 48426 no. exposed pairs = 3126 no. arc points = 21113 no. surface atoms = 1049 nbur = 1367 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 477 mr = 3885 m= 6 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1953 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8467 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4757699E-09 2.5107152E-08 midg,1,midg; midg,igrid,midg 2.6979331E-08 -7.5702546E-09 1,midg,midg; igrid,midg,midg 5.8014091E-08 -4.4459124E-08 gauss-seidel spectral radius is 0.9886039 estimated iterations to convergence 76 setup time was (sec) 0.3700000 now iterating at: 14:01:57 rms-change max change #iterations 0.1842109 27.37138 at 10iterations 2.1080883E-02 3.283871 at 20iterations 2.8448161E-03 0.4451780 at 30iterations 6.2067027E-04 0.1037827 at 40iterations 1.9666270E-04 3.2966614E-02 at 50iterations finished qdiffx linear iterations at : 14:02:00 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.9666270E-04 3.2966614E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:02:01 3.319u 0.169s 0:04.95 70.1% 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 14:02:01 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 2.025221 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): -14.33400 38.40100 ymin,ymax (A): 0.3790001 44.61300 zmin,zma (A): -7.211000 43.79800 x,y,z range (A): 52.73500 44.23400 51.00900 scale (grids/A): 2.025221 object centre (A): 12.03350 22.49600 18.29350 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 373.0131 centred at (gu) : 91.67916 93.12724 90.67121 assigned negative charge : -369.5135 centred at (gu) : 92.25049 93.34189 90.56021 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21113 grid for indexing accessible points = 1.400000 m= 29847 mr = 53007 m= 5421 mr = 21894 m= 400 mr = 3456 m= 11 mr = 173 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 281 time to turn everything in is 0.3900000 number of dielectric boundary points 34048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17994 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) : 0.6750735 object centre at (A) : 12.03350 22.49600 18.29350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0907525E-02 2.1327958E-02 midg,1,midg; midg,igrid,midg 3.4135524E-02 2.9299927E-03 1,midg,midg; igrid,midg,midg 2.1390222E-02 -5.7550911E-02 gauss-seidel spectral radius is 0.9987687 estimated iterations to convergence 226 setup time was (sec) 0.6000000 now iterating at: 14:02:02 rms-change max change #iterations 4.707507 210.5923 at 10iterations 2.283358 74.01961 at 20iterations 1.113292 34.22867 at 30iterations 0.5415044 17.01611 at 40iterations 0.2639041 7.791918 at 50iterations 0.1287614 3.901207 at 60iterations 6.2898315E-02 1.882793 at 70iterations 3.0795228E-02 0.9077568 at 80iterations 1.5130555E-02 0.4956589 at 90iterations 7.5511644E-03 0.2258091 at 100iterations 3.8597616E-03 0.1411209 at 110iterations 2.0318113E-03 6.2719345E-02 at 120iterations finished qdiffx linear iterations at : 14:02:09 total time elapsed so far: 7.560000 # loops : 120 mean,max change (kT/e) : 2.0318113E-03 6.2719345E-02 energy calculations done at 7.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 14:02:10 7.690u 0.193s 0:09.03 87.2% 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 14:02:10 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2416 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: 3.037831 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): -14.33400 38.40100 ymin,ymax (A): 0.3790001 44.61300 zmin,zma (A): -7.211000 43.79800 x,y,z range (A): 52.73500 44.23400 51.00900 scale (grids/A): 3.037831 object centre (A): 12.03350 22.49600 18.29350 number of atom coordinates read : 2416 total number of charged atoms : 2274 net assigned charge : 3.500024 assigned positive charge : 373.0131 centred at (gu) : 92.51860 94.69085 91.00677 assigned negative charge : -369.5135 centred at (gu) : 93.37554 95.01279 90.84031 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 177433 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21113 grid for indexing accessible points = 1.400000 m= 92923 mr = 128312 m= 37151 mr = 75634 m= 10092 mr = 29854 m= 1776 mr = 7582 m= 208 mr = 1190 m= 6 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 905 time to turn everything in is 1.030000 number of dielectric boundary points 76889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18192 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) : 2.025221 object centre at (A) : 12.03350 22.49600 18.29350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3168921 0.2004810 midg,1,midg; midg,igrid,midg 0.3284682 -8.4379129E-02 1,midg,midg; igrid,midg,midg 0.3852751 -0.6251197 gauss-seidel spectral radius is 0.9992872 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 14:02:12 rms-change max change #iterations 10.81383 444.9279 at 10iterations 6.410951 137.6080 at 20iterations 3.789682 72.58590 at 30iterations 2.229891 44.34042 at 40iterations 1.311382 24.30899 at 50iterations 0.7684308 13.70080 at 60iterations 0.4517308 7.817894 at 70iterations 0.2629972 5.178079 at 80iterations 0.1539851 3.066640 at 90iterations 9.0259209E-02 1.619390 at 100iterations 5.2814573E-02 0.9072037 at 110iterations 3.1068208E-02 0.6008835 at 120iterations 1.8367639E-02 0.3578701 at 130iterations 1.1053138E-02 0.2069321 at 140iterations 6.8246233E-03 0.1538887 at 150iterations 4.4009723E-03 9.7778320E-02 at 160iterations 2.9850239E-03 6.6452026E-02 at 170iterations 2.1465160E-03 5.0304413E-02 at 180iterations finished qdiffx linear iterations at : 14:02:23 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 2.1465160E-03 5.0304413E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 14:02:23 12.513u 0.209s 0:13.04 97.4% 0+0k 0+0io 0pf+0w