Sun Oct 9 00:40:51 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 00:40:51 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2161 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6616116 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): -0.1660000 53.64200 ymin,ymax (A): -14.85500 27.46100 zmin,zma (A): 32.59300 84.79900 x,y,z range (A): 53.80800 42.31600 52.20600 scale (grids/A): 0.6616116 object centre (A): 26.73800 6.303000 58.69600 number of atom coordinates read : 2161 total number of charged atoms : 2027 net assigned charge : 11.50002 assigned positive charge : 315.9888 centred at (gu) : 90.25544 88.40842 88.66430 assigned negative charge : -304.4893 centred at (gu) : 90.27263 88.49741 88.68555 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6566 nv = 96 ne = 84 npr = 43007 no. pairs analyzed = 43007 no. exposed pairs = 2870 no. arc points = 20761 no. surface atoms = 962 nbur = 1199 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3412 m= 5 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2050 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7597 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3951406E-08 2.0505547E-08 midg,1,midg; midg,igrid,midg 6.1477053E-08 1.1603048E-08 1,midg,midg; igrid,midg,midg 3.1226929E-08 2.8756929E-08 gauss-seidel spectral radius is 0.9881270 estimated iterations to convergence 75 setup time was (sec) 0.5300000 now iterating at: 00:40:52 rms-change max change #iterations 0.1463292 23.72804 at 10iterations 1.5505916E-02 2.220795 at 20iterations 1.6730349E-03 0.2399445 at 30iterations 1.9287807E-04 2.5520325E-02 at 40iterations 2.6754089E-05 3.6411285E-03 at 50iterations finished qdiffx linear iterations at : 00:40:55 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.6754089E-05 3.6411285E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 00:40:55 4.127u 0.215s 0:04.64 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 00:40:55 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2161 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.984835 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): -0.1660000 53.64200 ymin,ymax (A): -14.85500 27.46100 zmin,zma (A): 32.59300 84.79900 x,y,z range (A): 53.80800 42.31600 52.20600 scale (grids/A): 1.984835 object centre (A): 26.73800 6.303000 58.69600 number of atom coordinates read : 2161 total number of charged atoms : 2027 net assigned charge : 11.50002 assigned positive charge : 315.9888 centred at (gu) : 90.76618 85.22531 85.99293 assigned negative charge : -304.4893 centred at (gu) : 90.81814 85.49229 86.05685 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 69541 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20761 grid for indexing accessible points = 1.400000 m= 25512 mr = 46564 m= 4434 mr = 18234 m= 302 mr = 2649 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 353 time to turn everything in is 0.5900000 number of dielectric boundary points 32253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 16010 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) : 0.6616116 object centre at (A) : 26.73800 6.303000 58.69600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8963448E-02 4.0972069E-02 midg,1,midg; midg,igrid,midg 3.7227139E-02 -3.9720483E-04 1,midg,midg; igrid,midg,midg 5.9090003E-02 6.2440079E-02 gauss-seidel spectral radius is 0.9987022 estimated iterations to convergence 220 setup time was (sec) 0.9200000 now iterating at: 00:40:57 rms-change max change #iterations 3.979620 210.3061 at 10iterations 1.895106 84.42474 at 20iterations 0.9012333 32.79702 at 30iterations 0.4298715 14.79502 at 40iterations 0.2050977 6.713667 at 50iterations 9.7407974E-02 3.217007 at 60iterations 4.6642128E-02 1.501414 at 70iterations 2.2228682E-02 0.7059250 at 80iterations 1.0588679E-02 0.3597641 at 90iterations 5.0437525E-03 0.1690626 at 100iterations 2.4085289E-03 7.8544617E-02 at 110iterations 1.1512008E-03 3.5881042E-02 at 120iterations finished qdiffx linear iterations at : 00:41:05 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 1.1512008E-03 3.5881042E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 00:41:06 9.630u 0.248s 0:10.14 97.3% 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 00:41:06 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2161 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: 2.977252 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): -0.1660000 53.64200 ymin,ymax (A): -14.85500 27.46100 zmin,zma (A): 32.59300 84.79900 x,y,z range (A): 53.80800 42.31600 52.20600 scale (grids/A): 2.977252 object centre (A): 26.73800 6.303000 58.69600 number of atom coordinates read : 2161 total number of charged atoms : 2027 net assigned charge : 11.50002 assigned positive charge : 315.9888 centred at (gu) : 91.14929 82.83791 83.98933 assigned negative charge : -304.4893 centred at (gu) : 91.22719 83.23853 84.08545 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 160555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20761 grid for indexing accessible points = 1.400000 m= 80679 mr = 113098 m= 30781 mr = 64645 m= 7951 mr = 24268 m= 1263 mr = 5673 m= 78 mr = 801 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1205 time to turn everything in is 1.480000 number of dielectric boundary points 72803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 16210 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) : 1.984835 object centre at (A) : 26.73800 6.303000 58.69600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2869272 0.5167895 midg,1,midg; midg,igrid,midg 0.3293216 -3.7775040E-03 1,midg,midg; igrid,midg,midg 0.5847332 0.5830498 gauss-seidel spectral radius is 0.9992799 estimated iterations to convergence 294 setup time was (sec) 1.820000 now iterating at: 00:41:08 rms-change max change #iterations 9.470682 446.9415 at 10iterations 5.584618 142.7173 at 20iterations 3.290229 83.86295 at 30iterations 1.927014 46.55547 at 40iterations 1.128112 27.60752 at 50iterations 0.6605463 14.29352 at 60iterations 0.3849933 7.759722 at 70iterations 0.2240739 4.998062 at 80iterations 0.1300360 2.387857 at 90iterations 7.5730652E-02 1.553174 at 100iterations 4.3974470E-02 0.9074097 at 110iterations 2.5552073E-02 0.4750896 at 120iterations 1.4814863E-02 0.2913837 at 130iterations 8.5826954E-03 0.1599555 at 140iterations 5.0054817E-03 9.8914385E-02 at 150iterations 2.8958656E-03 5.6854248E-02 at 160iterations 1.6888798E-03 3.4629822E-02 at 170iterations 9.8398759E-04 1.7232895E-02 at 180iterations finished qdiffx linear iterations at : 00:41:21 total time elapsed so far: 15.31000 # loops : 180 mean,max change (kT/e) : 9.8398759E-04 1.7232895E-02 energy calculations done at 15.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 00:41:22 15.493u 0.303s 0:16.17 97.6% 0+0k 0+0io 0pf+0w