Mon Oct 10 23:38:57 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 23:38:58 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5914603 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): 10.51400 64.98100 ymin,ymax (A): -3.900000 56.29000 zmin,zma (A): 10.59500 54.06100 x,y,z range (A): 54.46700 60.19000 43.46600 scale (grids/A): 0.5914603 object centre (A): 37.74750 26.19500 32.32800 number of atom coordinates read : 2607 total number of charged atoms : 2462 net assigned charge : 7.906022 assigned positive charge : 392.3689 centred at (gu) : 88.74144 92.35352 89.48871 assigned negative charge : -384.4634 centred at (gu) : 88.70896 92.10356 89.64171 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5971 nv = 96 ne = 84 npr = 52580 no. pairs analyzed = 52580 no. exposed pairs = 3156 no. arc points = 22275 no. surface atoms = 1070 nbur = 1537 mkacc time = 0.1100000 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 = 1.456000 m= 249 mr = 3257 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3100000 number of dielectric boundary points 2940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2154 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7478 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2862578E-09 -1.6907417E-09 midg,1,midg; midg,igrid,midg -2.6913849E-09 1.5639735E-08 1,midg,midg; igrid,midg,midg 1.9125104E-09 2.4470619E-09 gauss-seidel spectral radius is 0.9852065 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 23:38:58 rms-change max change #iterations 0.1028128 15.37674 at 10iterations 9.9612875E-03 1.696114 at 20iterations 1.5046524E-03 0.3439636 at 30iterations 4.0641261E-04 0.1035004 at 40iterations 1.2210826E-04 3.1501770E-02 at 50iterations finished qdiffx linear iterations at : 23:39:01 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.2210826E-04 3.1501770E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 23:39:01 3.113u 0.163s 0:03.76 86.9% 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 23:39:01 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.774381 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): 10.51400 64.98100 ymin,ymax (A): -3.900000 56.29000 zmin,zma (A): 10.59500 54.06100 x,y,z range (A): 54.46700 60.19000 43.46600 scale (grids/A): 1.774381 object centre (A): 37.74750 26.19500 32.32800 number of atom coordinates read : 2607 total number of charged atoms : 2462 net assigned charge : 7.906022 assigned positive charge : 392.3689 centred at (gu) : 86.22364 97.06026 88.46555 assigned negative charge : -384.4634 centred at (gu) : 86.12663 96.31042 88.92477 start vw surface at 0.2400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 65336 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22275 grid for indexing accessible points = 1.400000 m= 22446 mr = 45404 m= 3012 mr = 16593 m= 105 mr = 1779 m= 0 mr = 15 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 872 time to turn everything in is 0.5500000 number of dielectric boundary points 27108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19165 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) : 0.5914603 object centre at (A) : 37.74750 26.19500 32.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3307534E-02 2.8531398E-03 midg,1,midg; midg,igrid,midg -1.2042351E-02 2.3564212E-02 1,midg,midg; igrid,midg,midg -5.1938463E-03 1.4144276E-02 gauss-seidel spectral radius is 0.9984254 estimated iterations to convergence 200 setup time was (sec) 0.8300000 now iterating at: 23:39:02 rms-change max change #iterations 3.691042 172.7635 at 10iterations 1.625446 62.74826 at 20iterations 0.7209319 27.44447 at 30iterations 0.3199677 11.12509 at 40iterations 0.1419520 4.648712 at 50iterations 6.3572578E-02 2.228736 at 60iterations 2.8173979E-02 0.9825439 at 70iterations 1.2646048E-02 0.4508095 at 80iterations 5.7633664E-03 0.2179871 at 90iterations 2.7253223E-03 0.1069946 at 100iterations 1.3454538E-03 5.3638458E-02 at 110iterations 6.9960282E-04 3.0654907E-02 at 120iterations finished qdiffx linear iterations at : 23:39:09 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 6.9960282E-04 3.0654907E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 23:39:09 7.249u 0.174s 0:07.75 95.6% 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 23:39:09 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 !!! WARNING: GLM 262 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.661572 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): 10.51400 64.98100 ymin,ymax (A): -3.900000 56.29000 zmin,zma (A): 10.59500 54.06100 x,y,z range (A): 54.46700 60.19000 43.46600 scale (grids/A): 2.661572 object centre (A): 37.74750 26.19500 32.32800 number of atom coordinates read : 2607 total number of charged atoms : 2462 net assigned charge : 7.906022 assigned positive charge : 392.3689 centred at (gu) : 84.33550 100.5902 87.69805 assigned negative charge : -384.4634 centred at (gu) : 84.18988 99.46564 88.38708 start vw surface at 0.2100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 151246 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22275 grid for indexing accessible points = 1.400000 m= 74502 mr = 110164 m= 25024 mr = 60999 m= 5091 mr = 20045 m= 447 mr = 3788 m= 13 mr = 226 m= 0 mr = 1 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 3103 time to turn everything in is 1.170000 number of dielectric boundary points 61100 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 19693 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) : 1.774381 object centre at (A) : 37.74750 26.19500 32.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2790987 4.6927381E-02 midg,1,midg; midg,igrid,midg -0.2453498 -0.1370652 1,midg,midg; igrid,midg,midg -0.1047341 0.1130510 gauss-seidel spectral radius is 0.9991958 estimated iterations to convergence 278 setup time was (sec) 1.440000 now iterating at: 23:39:11 rms-change max change #iterations 8.951451 305.3685 at 10iterations 5.071047 152.6389 at 20iterations 2.866832 66.20580 at 30iterations 1.622277 37.15876 at 40iterations 0.9120781 17.86797 at 50iterations 0.5147932 10.20552 at 60iterations 0.2896896 6.594944 at 70iterations 0.1627521 3.217333 at 80iterations 9.1515101E-02 1.782698 at 90iterations 5.1489003E-02 0.9673195 at 100iterations 2.9008720E-02 0.5903625 at 110iterations 1.6352097E-02 0.3547897 at 120iterations 9.2729414E-03 0.2136421 at 130iterations 5.3117564E-03 0.1196327 at 140iterations 3.0916347E-03 7.4375153E-02 at 150iterations 1.8451409E-03 4.3640137E-02 at 160iterations 1.1487753E-03 2.9182434E-02 at 170iterations 7.4448338E-04 1.8535614E-02 at 180iterations finished qdiffx linear iterations at : 23:39:20 total time elapsed so far: 11.02000 # loops : 180 mean,max change (kT/e) : 7.4448338E-04 1.8535614E-02 energy calculations done at 11.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 23:39:21 11.204u 0.193s 0:11.86 96.0% 0+0k 0+0io 0pf+0w