Sun Oct 9 16:20:58 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 16:20:58 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 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: 0.6235004 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): -21.21000 35.09000 ymin,ymax (A): 54.47900 106.5420 zmin,zma (A): -1.523000 55.57400 x,y,z range (A): 56.30000 52.06300 57.09700 scale (grids/A): 0.6235004 object centre (A): 6.940001 80.51050 27.02550 number of atom coordinates read : 3038 total number of charged atoms : 2896 net assigned charge : -2.499988 assigned positive charge : 454.0990 centred at (gu) : 91.03748 90.26357 90.08055 assigned negative charge : -456.6003 centred at (gu) : 91.06688 90.15031 90.21477 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7778 nv = 96 ne = 84 npr = 61511 no. pairs analyzed = 61511 no. exposed pairs = 3981 no. arc points = 27816 no. surface atoms = 1336 nbur = 1702 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 4068 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2100000 number of dielectric boundary points 4122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2658 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0541477E-09 -1.4243595E-08 midg,1,midg; midg,igrid,midg -1.1442418E-08 7.9189668E-09 1,midg,midg; igrid,midg,midg 2.3405866E-10 -5.9779426E-09 gauss-seidel spectral radius is 0.9867193 estimated iterations to convergence 71 setup time was (sec) 0.4000000 now iterating at: 16:20:58 rms-change max change #iterations 0.1371683 19.02447 at 10iterations 1.2873139E-02 2.180936 at 20iterations 1.2718982E-03 0.1743717 at 30iterations 1.9036423E-04 2.1790981E-02 at 40iterations 5.0545375E-05 5.2986145E-03 at 50iterations finished qdiffx linear iterations at : 16:21:01 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.0545375E-05 5.2986145E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 16:21:02 3.370u 0.185s 0:03.90 91.0% 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 16:21:02 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 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: 1.870501 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): -21.21000 35.09000 ymin,ymax (A): 54.47900 106.5420 zmin,zma (A): -1.523000 55.57400 x,y,z range (A): 56.30000 52.06300 57.09700 scale (grids/A): 1.870501 object centre (A): 6.940001 80.51050 27.02550 number of atom coordinates read : 3038 total number of charged atoms : 2896 net assigned charge : -2.499988 assigned positive charge : 454.0990 centred at (gu) : 93.11169 90.78963 90.24125 assigned negative charge : -456.6003 centred at (gu) : 93.20058 90.45095 90.64380 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 29177 mr = 57179 m= 4744 mr = 20352 m= 256 mr = 2889 m= 0 mr = 99 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1486 time to turn everything in is 0.4100000 number of dielectric boundary points 37952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 22726 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) : 0.6235004 object centre at (A) : 6.940001 80.51050 27.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6894506E-02 -2.0668406E-02 midg,1,midg; midg,igrid,midg -1.9156361E-02 -9.7760884E-03 1,midg,midg; igrid,midg,midg -9.8406496E-03 -4.3255288E-02 gauss-seidel spectral radius is 0.9986368 estimated iterations to convergence 215 setup time was (sec) 0.6300000 now iterating at: 16:21:03 rms-change max change #iterations 4.478589 172.4418 at 10iterations 2.083960 65.09548 at 20iterations 0.9757907 28.85055 at 30iterations 0.4582219 13.80153 at 40iterations 0.2132955 7.253153 at 50iterations 0.1004652 3.157398 at 60iterations 4.6872936E-02 1.353942 at 70iterations 2.1975771E-02 0.6559019 at 80iterations 1.0282820E-02 0.3198242 at 90iterations 4.8290011E-03 0.1454353 at 100iterations 2.2772306E-03 6.7539215E-02 at 110iterations 1.0733650E-03 3.1523228E-02 at 120iterations finished qdiffx linear iterations at : 16:21:10 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 1.0733650E-03 3.1523228E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 16:21:10 7.843u 0.192s 0:08.32 96.5% 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 16:21:10 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 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: 2.805752 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): -21.21000 35.09000 ymin,ymax (A): 54.47900 106.5420 zmin,zma (A): -1.523000 55.57400 x,y,z range (A): 56.30000 52.06300 57.09700 scale (grids/A): 2.805752 object centre (A): 6.940001 80.51050 27.02550 number of atom coordinates read : 3038 total number of charged atoms : 2896 net assigned charge : -2.499988 assigned positive charge : 454.0990 centred at (gu) : 94.66753 91.18421 90.36179 assigned negative charge : -456.6003 centred at (gu) : 94.80086 90.67638 90.96577 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 195286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27816 grid for indexing accessible points = 1.400000 m= 94014 mr = 139173 m= 33857 mr = 74405 m= 8518 mr = 26505 m= 1215 mr = 6354 m= 64 mr = 816 m= 0 mr = 22 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 5033 time to turn everything in is 1.050000 number of dielectric boundary points 85679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 23166 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) : 1.870501 object centre at (A) : 6.940001 80.51050 27.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8850794 -0.2873947 midg,1,midg; midg,igrid,midg -0.2022216 -0.2829714 1,midg,midg; igrid,midg,midg -0.1310760 -0.5932454 gauss-seidel spectral radius is 0.9992773 estimated iterations to convergence 294 setup time was (sec) 1.280000 now iterating at: 16:21:12 rms-change max change #iterations 10.77055 317.4263 at 10iterations 6.446130 148.8970 at 20iterations 3.828865 88.39075 at 30iterations 2.258639 50.32574 at 40iterations 1.327506 29.51091 at 50iterations 0.7781015 15.86567 at 60iterations 0.4552477 10.52560 at 70iterations 0.2653016 4.876084 at 80iterations 0.1550009 2.803613 at 90iterations 9.0293422E-02 1.866315 at 100iterations 5.2594103E-02 1.056702 at 110iterations 3.0526012E-02 0.6486373 at 120iterations 1.7726405E-02 0.3493958 at 130iterations 1.0303836E-02 0.1754169 at 140iterations 5.9710578E-03 0.1170959 at 150iterations 3.4707100E-03 6.9720268E-02 at 160iterations 2.0100605E-03 3.6634445E-02 at 170iterations 1.1654111E-03 2.0416260E-02 at 180iterations finished qdiffx linear iterations at : 16:21:23 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.1654111E-03 2.0416260E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 16:21:23 12.822u 0.215s 0:13.30 97.9% 0+0k 0+0io 0pf+0w