Mon Oct 10 09:10:07 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 09:10:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6325403 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 0.6325403 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 289.8650 centred at (gu) : 90.64653 90.01088 90.52849 assigned negative charge : -286.8653 centred at (gu) : 90.56129 90.15572 90.52657 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5286 nv = 96 ne = 84 npr = 40489 no. pairs analyzed = 40489 no. exposed pairs = 2459 no. arc points = 17140 no. surface atoms = 835 nbur = 1127 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2924 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1677 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0010114E-09 4.0419570E-09 midg,1,midg; midg,igrid,midg 1.3458680E-08 -6.8655241E-09 1,midg,midg; igrid,midg,midg -2.1948754E-09 1.0828932E-08 gauss-seidel spectral radius is 0.9869965 estimated iterations to convergence 72 setup time was (sec) 0.4800000 now iterating at: 09:10:07 rms-change max change #iterations 0.1187551 20.49202 at 10iterations 1.1415316E-02 1.739933 at 20iterations 1.0856952E-03 0.1945210 at 30iterations 1.0337587E-04 1.8994331E-02 at 40iterations 9.8390901E-06 1.5754700E-03 at 50iterations finished qdiffx linear iterations at : 09:10:10 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 9.8390901E-06 1.5754700E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 09:10:11 3.213u 0.164s 0:03.72 90.5% 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 Mon Oct 10 2011 at 09:10:11 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.897621 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 1.897621 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 289.8650 centred at (gu) : 91.93967 90.03277 91.58535 assigned negative charge : -286.8653 centred at (gu) : 91.68404 90.46726 91.57979 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 56849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17140 grid for indexing accessible points = 1.400000 m= 21227 mr = 39111 m= 3375 mr = 16092 m= 188 mr = 2164 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 24216 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14286 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) : 0.6325403 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3958193E-02 3.4219414E-02 midg,1,midg; midg,igrid,midg 3.1893176E-03 -9.3915323E-03 1,midg,midg; igrid,midg,midg -4.1193739E-03 -1.6135599E-03 gauss-seidel spectral radius is 0.9985487 estimated iterations to convergence 208 setup time was (sec) 0.7100000 now iterating at: 09:10:11 rms-change max change #iterations 3.581151 167.2186 at 10iterations 1.642627 65.77698 at 20iterations 0.7515263 27.26459 at 30iterations 0.3437665 12.03159 at 40iterations 0.1570217 5.508288 at 50iterations 7.1950026E-02 2.649813 at 60iterations 3.2789793E-02 1.326110 at 70iterations 1.5035695E-02 0.5670221 at 80iterations 6.8370765E-03 0.2498131 at 90iterations 3.1374749E-03 0.1083984 at 100iterations 1.4311343E-03 5.4428577E-02 at 110iterations 6.5667677E-04 2.4110794E-02 at 120iterations finished qdiffx linear iterations at : 09:10:18 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 6.5667677E-04 2.4110794E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 09:10:18 7.176u 0.205s 0:07.66 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 09:10:18 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.846431 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): -35.04000 9.719001 ymin,ymax (A): -0.5870000 40.95700 zmin,zma (A): -0.9170000 55.36400 x,y,z range (A): 44.75900 41.54400 56.28100 scale (grids/A): 2.846431 object centre (A): -12.66050 20.18500 27.22350 number of atom coordinates read : 1962 total number of charged atoms : 1819 net assigned charge : 3.000004 assigned positive charge : 289.8650 centred at (gu) : 92.90942 90.04913 92.37807 assigned negative charge : -286.8653 centred at (gu) : 92.52611 90.70097 92.36977 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 131515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17140 grid for indexing accessible points = 1.400000 m= 68171 mr = 94760 m= 25422 mr = 56434 m= 6075 mr = 20967 m= 853 mr = 4624 m= 57 mr = 602 m= 4 mr = 28 m= 0 mr = 2 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 54680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 14543 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) : 1.897621 object centre at (A) : -12.66050 20.18500 27.22350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6298364E-02 0.1955161 midg,1,midg; midg,igrid,midg -3.2677617E-02 -0.1322598 1,midg,midg; igrid,midg,midg -7.2030470E-02 -7.0013553E-02 gauss-seidel spectral radius is 0.9992187 estimated iterations to convergence 282 setup time was (sec) 1.340000 now iterating at: 09:10:20 rms-change max change #iterations 8.388337 393.1484 at 10iterations 4.777045 101.0382 at 20iterations 2.707172 63.67795 at 30iterations 1.533990 44.23835 at 40iterations 0.8665763 20.90998 at 50iterations 0.4902068 10.08497 at 60iterations 0.2767407 5.626282 at 70iterations 0.1561238 3.445778 at 80iterations 8.8325985E-02 1.793186 at 90iterations 4.9863715E-02 0.9870081 at 100iterations 2.8267032E-02 0.5996361 at 110iterations 1.5916422E-02 0.3652916 at 120iterations 9.0034800E-03 0.1792617 at 130iterations 5.0722728E-03 9.8115921E-02 at 140iterations 2.8692617E-03 5.5431366E-02 at 150iterations 1.6195733E-03 3.2709122E-02 at 160iterations 9.1370760E-04 1.8715873E-02 at 170iterations 5.1629217E-04 1.1250019E-02 at 180iterations finished qdiffx linear iterations at : 09:10:30 total time elapsed so far: 11.19000 # loops : 180 mean,max change (kT/e) : 5.1629217E-04 1.1250019E-02 energy calculations done at 11.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 09:10:30 11.368u 0.216s 0:11.86 97.5% 0+0k 0+0io 0pf+0w