Sun Oct 9 21:08:11 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 Sun Oct 9 2011 at 21:08:11 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 = 2576 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: 0.6387598 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): 10.45600 66.18900 ymin,ymax (A): -11.95400 37.01000 zmin,zma (A): -11.75300 41.21700 x,y,z range (A): 55.73300 48.96400 52.97000 scale (grids/A): 0.6387598 object centre (A): 38.32250 12.52800 14.73200 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 90.58332 91.13964 90.14414 assigned negative charge : -383.4987 centred at (gu) : 90.63187 91.08855 90.17659 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 51926 no. pairs analyzed = 51926 no. exposed pairs = 3064 no. arc points = 21847 no. surface atoms = 1035 nbur = 1541 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3753 m= 0 mr = 31 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 102 time to turn everything in is 0.2000000 number of dielectric boundary points 3437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8412 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0267108E-08 3.4566465E-09 midg,1,midg; midg,igrid,midg 1.0630048E-09 1.6123872E-08 1,midg,midg; igrid,midg,midg 1.0927644E-08 1.7094105E-09 gauss-seidel spectral radius is 0.9873005 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 21:08:12 rms-change max change #iterations 0.1450594 22.00584 at 10iterations 1.4406316E-02 2.139208 at 20iterations 1.4079219E-03 0.1984940 at 30iterations 1.3882444E-04 2.0927429E-02 at 40iterations 1.4072455E-05 1.9993782E-03 at 50iterations finished qdiffx linear iterations at : 21:08:15 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.4072455E-05 1.9993782E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 21:08:15 3.432u 0.168s 0:03.87 92.7% 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 21:08:15 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 = 2576 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: 1.916279 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): 10.45600 66.18900 ymin,ymax (A): -11.95400 37.01000 zmin,zma (A): -11.75300 41.21700 x,y,z range (A): 55.73300 48.96400 52.97000 scale (grids/A): 1.916279 object centre (A): 38.32250 12.52800 14.73200 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 91.74957 93.41832 90.43176 assigned negative charge : -383.4987 centred at (gu) : 91.89528 93.26556 90.52957 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21847 grid for indexing accessible points = 1.400000 m= 25305 mr = 51888 m= 3764 mr = 18370 m= 240 mr = 2371 m= 3 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1758 time to turn everything in is 0.3700000 number of dielectric boundary points 31616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 19161 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) : 0.6387598 object centre at (A) : 38.32250 12.52800 14.73200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3759942E-02 -7.6862928E-03 midg,1,midg; midg,igrid,midg -1.2864069E-02 8.8586127E-03 1,midg,midg; igrid,midg,midg 1.4253209E-02 3.2983594E-02 gauss-seidel spectral radius is 0.9986429 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 21:08:16 rms-change max change #iterations 4.215902 178.0194 at 10iterations 1.974708 74.54356 at 20iterations 0.9270308 30.88170 at 30iterations 0.4339576 12.93326 at 40iterations 0.2034160 7.031614 at 50iterations 9.5874973E-02 3.009247 at 60iterations 4.4720519E-02 1.309120 at 70iterations 2.1028040E-02 0.6210632 at 80iterations 9.8778596E-03 0.2967775 at 90iterations 4.6287640E-03 0.1481967 at 100iterations 2.1788366E-03 6.9578171E-02 at 110iterations 1.0197511E-03 3.4795761E-02 at 120iterations finished qdiffx linear iterations at : 21:08:23 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.0197511E-03 3.4795761E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 21:08:23 7.808u 0.208s 0:08.28 96.6% 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 Sun Oct 9 2011 at 21:08:23 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 = 2576 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: 2.874419 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): 10.45600 66.18900 ymin,ymax (A): -11.95400 37.01000 zmin,zma (A): -11.75300 41.21700 x,y,z range (A): 55.73300 48.96400 52.97000 scale (grids/A): 2.874419 object centre (A): 38.32250 12.52800 14.73200 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 388.4979 centred at (gu) : 92.62427 95.12742 90.64755 assigned negative charge : -383.4987 centred at (gu) : 92.84296 94.89814 90.79440 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 173690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21847 grid for indexing accessible points = 1.400000 m= 83578 mr = 125400 m= 28312 mr = 68291 m= 6659 mr = 22329 m= 1073 mr = 5101 m= 56 mr = 774 m= 0 mr = 23 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 5895 time to turn everything in is 0.9300000 number of dielectric boundary points 71450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19456 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) : 1.916279 object centre at (A) : 38.32250 12.52800 14.73200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2249071 -0.2251190 midg,1,midg; midg,igrid,midg -0.2418457 0.1212772 1,midg,midg; igrid,midg,midg 0.2666812 0.3013012 gauss-seidel spectral radius is 0.9992593 estimated iterations to convergence 290 setup time was (sec) 1.160000 now iterating at: 21:08:25 rms-change max change #iterations 9.848125 369.8324 at 10iterations 5.706158 115.5070 at 20iterations 3.295013 61.25510 at 30iterations 1.896851 34.59800 at 40iterations 1.090514 22.01706 at 50iterations 0.6274567 11.45663 at 60iterations 0.3600823 6.553583 at 70iterations 0.2068330 3.693198 at 80iterations 0.1189453 2.192055 at 90iterations 6.8196215E-02 1.259348 at 100iterations 3.9094221E-02 0.7204332 at 110iterations 2.2406187E-02 0.3908501 at 120iterations 1.2867047E-02 0.2236557 at 130iterations 7.3797316E-03 0.1336432 at 140iterations 4.2370437E-03 7.6030254E-02 at 150iterations 2.4283847E-03 4.4071198E-02 at 160iterations 1.3960537E-03 2.6275635E-02 at 170iterations 8.0156856E-04 1.4154911E-02 at 180iterations finished qdiffx linear iterations at : 21:08:36 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 8.0156856E-04 1.4154911E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 21:08:36 12.575u 0.217s 0:13.08 97.7% 0+0k 0+0io 0pf+0w