Mon Oct 10 11:06:11 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+sph.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 = amb.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 11:06:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5406 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5012249 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): 43.07000 114.0960 ymin,ymax (A): -29.90900 39.49200 zmin,zma (A): -32.76500 33.56500 x,y,z range (A): 71.02600 69.40100 66.33000 scale (grids/A): 0.5012249 object centre (A): 78.58300 4.791500 0.3999996 number of atom coordinates read : 5406 total number of charged atoms : 5249 net assigned charge : 8.500039 assigned positive charge : 854.1749 centred at (gu) : 90.72071 90.50082 91.09892 assigned negative charge : -845.6830 centred at (gu) : 90.68895 90.52628 91.10161 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8588 nv = 96 ne = 84 npr = 106698 no. pairs analyzed = 106698 no. exposed pairs = 6471 no. arc points = 44498 no. surface atoms = 2172 nbur = 3234 mkacc time = 0.2400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 284 mr = 4659 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.5200000 number of dielectric boundary points 4207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4394 ## 697 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 11619 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3081748E-11 9.7190596E-11 midg,1,midg; midg,igrid,midg 1.1398747E-10 2.9692769E-11 1,midg,midg; igrid,midg,midg 1.1563018E-11 1.7319794E-10 gauss-seidel spectral radius is 0.9796872 estimated iterations to convergence 58 setup time was (sec) 0.7600000 now iterating at: 11:06:12 rms-change max change #iterations 6.6364922E-02 9.636477 at 10iterations 3.6282027E-03 0.4919510 at 20iterations 5.4345373E-04 8.7835312E-02 at 30iterations 2.6025556E-04 3.9705038E-02 at 40iterations 1.3542315E-04 2.0817280E-02 at 50iterations finished qdiffx linear iterations at : 11:06:15 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 1.3542315E-04 2.0817280E-02 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 11:06:16 3.824u 0.208s 0:04.31 93.2% 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 11:06:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5406 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.503675 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): 43.07000 114.0960 ymin,ymax (A): -29.90900 39.49200 zmin,zma (A): -32.76500 33.56500 x,y,z range (A): 71.02600 69.40100 66.33000 scale (grids/A): 1.503675 object centre (A): 78.58300 4.791500 0.3999996 number of atom coordinates read : 5406 total number of charged atoms : 5249 net assigned charge : 8.500039 assigned positive charge : 854.1749 centred at (gu) : 92.16061 91.50043 93.29519 assigned negative charge : -845.6830 centred at (gu) : 92.06683 91.57895 93.30457 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 99099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28156 mr = 70318 m= 2197 mr = 19088 m= 37 mr = 941 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1131 time to turn everything in is 0.7200000 number of dielectric boundary points 39142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 693 ## 12 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 39186 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) : 0.5012249 object centre at (A) : 78.58300 4.791500 0.3999996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2914441E-03 1.5670032E-04 midg,1,midg; midg,igrid,midg 1.9877402E-02 -2.9836358E-03 1,midg,midg; igrid,midg,midg -2.3526033E-02 9.2481822E-03 gauss-seidel spectral radius is 0.9980795 estimated iterations to convergence 181 setup time was (sec) 1.050000 now iterating at: 11:06:17 rms-change max change #iterations 3.974614 143.2039 at 10iterations 1.616986 54.75665 at 20iterations 0.6583467 21.10447 at 30iterations 0.2681753 8.373388 at 40iterations 0.1094452 3.143681 at 50iterations 4.4654924E-02 1.560093 at 60iterations 1.8215345E-02 0.5928383 at 70iterations 7.4816630E-03 0.2399597 at 80iterations 3.0927549E-03 0.1064816 at 90iterations 1.3312809E-03 4.4784546E-02 at 100iterations 6.3156668E-04 2.4124146E-02 at 110iterations 3.6780105E-04 1.2822151E-02 at 120iterations finished qdiffx linear iterations at : 11:06:25 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 3.6780105E-04 1.2822151E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 11:06:25 9.092u 0.233s 0:09.59 97.1% 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 11:06:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5406 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: 2.255512 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): 43.07000 114.0960 ymin,ymax (A): -29.90900 39.49200 zmin,zma (A): -32.76500 33.56500 x,y,z range (A): 71.02600 69.40100 66.33000 scale (grids/A): 2.255512 object centre (A): 78.58300 4.791500 0.3999996 number of atom coordinates read : 5406 total number of charged atoms : 5249 net assigned charge : 8.500039 assigned positive charge : 854.1749 centred at (gu) : 93.24039 92.25042 94.94238 assigned negative charge : -845.6830 centred at (gu) : 93.10030 92.36837 94.95676 start vw surface at 0.2400000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 231707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44498 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 103066 mr = 172623 m= 24530 mr = 81830 m= 3028 mr = 17744 m= 131 mr = 1864 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 3912 time to turn everything in is 1.760000 number of dielectric boundary points 88357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 41829 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) : 1.503675 object centre at (A) : 78.58300 4.791500 0.3999996 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8099750E-02 -0.1307103 midg,1,midg; midg,igrid,midg 0.5906134 -9.9319629E-02 1,midg,midg; igrid,midg,midg -0.7349291 0.1414233 gauss-seidel spectral radius is 0.9991534 estimated iterations to convergence 271 setup time was (sec) 2.120000 now iterating at: 11:06:28 rms-change max change #iterations 10.81007 296.5064 at 10iterations 6.176209 141.1798 at 20iterations 3.489360 79.94471 at 30iterations 1.958443 40.30998 at 40iterations 1.097960 22.87928 at 50iterations 0.6133316 12.04755 at 60iterations 0.3417374 6.170000 at 70iterations 0.1902727 3.571560 at 80iterations 0.1056962 1.864555 at 90iterations 5.8701921E-02 1.111313 at 100iterations 3.2618202E-02 0.5755024 at 110iterations 1.8069034E-02 0.3120747 at 120iterations 1.0021566E-02 0.2042451 at 130iterations 5.5545219E-03 9.7480774E-02 at 140iterations 3.0805164E-03 5.4759979E-02 at 150iterations 1.7102219E-03 3.2967567E-02 at 160iterations 9.5097715E-04 1.9500732E-02 at 170iterations 5.3390383E-04 9.6931458E-03 at 180iterations finished qdiffx linear iterations at : 11:06:41 total time elapsed so far: 15.00000 # loops : 180 mean,max change (kT/e) : 5.3390383E-04 9.6931458E-03 energy calculations done at 15.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.20000 DelPhi exited at 11:06:41 15.201u 0.236s 0:15.71 98.2% 0+0k 0+0io 0pf+0w