Sun Oct 9 11:31:03 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 11:31:03 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2093 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6679550 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): -1.930000 51.36700 ymin,ymax (A): -26.24300 26.27000 zmin,zma (A): -2.016000 49.37700 x,y,z range (A): 53.29700 52.51300 51.39300 scale (grids/A): 0.6679550 object centre (A): 24.71850 1.3500214E-02 23.68050 number of atom coordinates read : 2093 total number of charged atoms : 1956 net assigned charge : -2.485982 assigned positive charge : 302.1347 centred at (gu) : 89.96089 91.96392 90.23517 assigned negative charge : -304.6213 centred at (gu) : 89.88488 91.86854 90.02042 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6503 nv = 96 ne = 84 npr = 41789 no. pairs analyzed = 41789 no. exposed pairs = 2897 no. arc points = 20279 no. surface atoms = 969 nbur = 1124 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3337 m= 1 mr = 71 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 0.1700000 number of dielectric boundary points 3510 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1869 ## 135 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7321 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7427442E-08 3.3143891E-08 midg,1,midg; midg,igrid,midg -1.7716971E-08 1.4930478E-08 1,midg,midg; igrid,midg,midg -2.2911708E-08 5.9972525E-09 gauss-seidel spectral radius is 0.9883473 estimated iterations to convergence 76 setup time was (sec) 0.3800000 now iterating at: 11:31:04 rms-change max change #iterations 0.1522833 23.98196 at 10iterations 1.6800120E-02 2.466393 at 20iterations 1.8115421E-03 0.2682610 at 30iterations 1.9531106E-04 2.5833130E-02 at 40iterations 2.1672231E-05 3.1929016E-03 at 50iterations finished qdiffx linear iterations at : 11:31:07 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 2.1672231E-05 3.1929016E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 11:31:07 3.611u 0.218s 0:04.09 93.3% 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 11:31:07 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2093 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.003865 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): -1.930000 51.36700 ymin,ymax (A): -26.24300 26.27000 zmin,zma (A): -2.016000 49.37700 x,y,z range (A): 53.29700 52.51300 51.39300 scale (grids/A): 2.003865 object centre (A): 24.71850 1.3500214E-02 23.68050 number of atom coordinates read : 2093 total number of charged atoms : 1956 net assigned charge : -2.485982 assigned positive charge : 302.1347 centred at (gu) : 89.88249 95.89159 90.70520 assigned negative charge : -304.6213 centred at (gu) : 89.65499 95.60563 90.06150 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20279 grid for indexing accessible points = 1.400000 m= 24805 mr = 45643 m= 4605 mr = 17760 m= 442 mr = 3070 m= 5 mr = 216 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 0.3600000 number of dielectric boundary points 32094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15463 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) : 0.6679550 object centre at (A) : 24.71850 1.3500214E-02 23.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8858184E-02 3.6967088E-02 midg,1,midg; midg,igrid,midg -1.0150072E-02 4.3645713E-02 1,midg,midg; igrid,midg,midg -3.0476853E-02 5.9748073E-03 gauss-seidel spectral radius is 0.9987215 estimated iterations to convergence 222 setup time was (sec) 0.6000000 now iterating at: 11:31:08 rms-change max change #iterations 4.105917 193.1183 at 10iterations 1.969958 70.02313 at 20iterations 0.9427013 35.09809 at 30iterations 0.4540999 17.73678 at 40iterations 0.2179883 7.296055 at 50iterations 0.1044433 3.578184 at 60iterations 5.0476089E-02 1.817808 at 70iterations 2.4097335E-02 0.8360069 at 80iterations 1.1575383E-02 0.3625293 at 90iterations 5.5358335E-03 0.1740055 at 100iterations 2.6719675E-03 8.4415913E-02 at 110iterations 1.2740812E-03 4.0406436E-02 at 120iterations finished qdiffx linear iterations at : 11:31:15 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 1.2740812E-03 4.0406436E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 11:31:16 8.170u 0.250s 0:08.77 96.0% 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 11:31:16 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2093 !!! WARNING: HIR 524 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.005798 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): -1.930000 51.36700 ymin,ymax (A): -26.24300 26.27000 zmin,zma (A): -2.016000 49.37700 x,y,z range (A): 53.29700 52.51300 51.39300 scale (grids/A): 3.005798 object centre (A): 24.71850 1.3500214E-02 23.68050 number of atom coordinates read : 2093 total number of charged atoms : 1956 net assigned charge : -2.485982 assigned positive charge : 302.1347 centred at (gu) : 89.82368 98.83748 91.05784 assigned negative charge : -304.6213 centred at (gu) : 89.48254 98.40852 90.09247 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 159367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20279 grid for indexing accessible points = 1.400000 m= 78079 mr = 111376 m= 30373 mr = 62379 m= 8751 mr = 24362 m= 1839 mr = 6741 m= 146 mr = 1383 m= 4 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 72273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 15643 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) : 2.003865 object centre at (A) : 24.71850 1.3500214E-02 23.68050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6897863 0.3971279 midg,1,midg; midg,igrid,midg -9.7501077E-02 0.3770379 1,midg,midg; igrid,midg,midg -0.3548661 -4.6296887E-02 gauss-seidel spectral radius is 0.9992838 estimated iterations to convergence 295 setup time was (sec) 1.190000 now iterating at: 11:31:17 rms-change max change #iterations 9.429558 403.0054 at 10iterations 5.492404 134.8350 at 20iterations 3.198651 73.01913 at 30iterations 1.864899 35.83937 at 40iterations 1.084203 23.07354 at 50iterations 0.6286941 12.26561 at 60iterations 0.3658555 6.990656 at 70iterations 0.2118923 3.894926 at 80iterations 0.1229251 2.273180 at 90iterations 7.1248360E-02 1.271168 at 100iterations 4.1191723E-02 0.7941017 at 110iterations 2.3939760E-02 0.4232168 at 120iterations 1.3879805E-02 0.2530899 at 130iterations 8.0359448E-03 0.1459045 at 140iterations 4.6716444E-03 8.4581852E-02 at 150iterations 2.6943283E-03 5.0096154E-02 at 160iterations 1.5632908E-03 2.9853821E-02 at 170iterations 9.0783834E-04 1.6378403E-02 at 180iterations finished qdiffx linear iterations at : 11:31:30 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 9.0783834E-04 1.6378403E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 11:31:30 13.758u 0.272s 0:14.34 97.7% 0+0k 0+0io 0pf+0w