Mon Oct 10 14:03:55 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 14:03:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2698 !!! WARNING: ZN5 590 has a net charge of 1.4000 !!! WARNING: ZN5 591 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5780253 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): -2.873000 50.16200 ymin,ymax (A): -7.220000 41.32200 zmin,zma (A): -13.99200 47.59700 x,y,z range (A): 53.03500 48.54200 61.58900 scale (grids/A): 0.5780253 object centre (A): 23.64450 17.05100 16.80250 number of atom coordinates read : 2698 total number of charged atoms : 2559 net assigned charge : 6.800004 assigned positive charge : 410.3224 centred at (gu) : 90.10321 89.58720 88.20880 assigned negative charge : -403.5234 centred at (gu) : 90.07224 89.47911 88.34423 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 53004 no. pairs analyzed = 53004 no. exposed pairs = 3448 no. arc points = 24308 no. surface atoms = 1156 nbur = 1542 mkacc time = 9.0000004E-02 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 = 1.484000 m= 285 mr = 3234 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3132 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2411 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7540 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8586642E-09 -7.8250478E-10 midg,1,midg; midg,igrid,midg -7.8042967E-10 3.0271383E-09 1,midg,midg; igrid,midg,midg 7.4585033E-10 1.9648820E-09 gauss-seidel spectral radius is 0.9845325 estimated iterations to convergence 66 setup time was (sec) 0.3900000 now iterating at: 14:03:56 rms-change max change #iterations 9.5970392E-02 16.86659 at 10iterations 7.5801397E-03 1.157461 at 20iterations 9.3061215E-04 0.1967983 at 30iterations 2.5337699E-04 6.1767578E-02 at 40iterations 8.4784835E-05 2.0473480E-02 at 50iterations finished qdiffx linear iterations at : 14:03:59 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.4784835E-05 2.0473480E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:03:59 3.357u 0.163s 0:03.96 88.6% 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 14:03:59 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 = 2698 !!! WARNING: ZN5 590 has a net charge of 1.4000 !!! WARNING: ZN5 591 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.734076 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): -2.873000 50.16200 ymin,ymax (A): -7.220000 41.32200 zmin,zma (A): -13.99200 47.59700 x,y,z range (A): 53.03500 48.54200 61.58900 scale (grids/A): 1.734076 object centre (A): 23.64450 17.05100 16.80250 number of atom coordinates read : 2698 total number of charged atoms : 2559 net assigned charge : 6.800004 assigned positive charge : 410.3224 centred at (gu) : 90.30880 88.76093 84.62556 assigned negative charge : -403.5234 centred at (gu) : 90.21648 88.43718 85.03254 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 66103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24308 grid for indexing accessible points = 1.400000 m= 22832 mr = 45176 m= 2884 mr = 16207 m= 119 mr = 1587 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 433 time to turn everything in is 0.3200000 number of dielectric boundary points 28960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 233 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 19837 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) : 0.5780253 object centre at (A) : 23.64450 17.05100 16.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9177225E-02 5.2920277E-03 midg,1,midg; midg,igrid,midg -4.6223854E-03 5.3539295E-03 1,midg,midg; igrid,midg,midg -1.3473843E-02 8.1864633E-03 gauss-seidel spectral radius is 0.9983747 estimated iterations to convergence 197 setup time was (sec) 0.5200000 now iterating at: 14:04:00 rms-change max change #iterations 3.592355 159.4405 at 10iterations 1.560334 57.87043 at 20iterations 0.6813051 26.27318 at 30iterations 0.2984138 10.86194 at 40iterations 0.1305625 4.688721 at 50iterations 5.7007004E-02 2.041623 at 60iterations 2.4977062E-02 0.8855329 at 70iterations 1.1101397E-02 0.3861957 at 80iterations 4.9437662E-03 0.1730347 at 90iterations 2.2835010E-03 9.2906952E-02 at 100iterations 1.1204403E-03 4.7092438E-02 at 110iterations 6.0684298E-04 2.6878357E-02 at 120iterations finished qdiffx linear iterations at : 14:04:07 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 6.0684298E-04 2.6878357E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:04:08 7.563u 0.208s 0:08.29 93.6% 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 14:04:08 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 = 2698 !!! WARNING: ZN5 590 has a net charge of 1.4000 !!! WARNING: ZN5 591 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.601114 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): -2.873000 50.16200 ymin,ymax (A): -7.220000 41.32200 zmin,zma (A): -13.99200 47.59700 x,y,z range (A): 53.03500 48.54200 61.58900 scale (grids/A): 2.601114 object centre (A): 23.64450 17.05100 16.80250 number of atom coordinates read : 2698 total number of charged atoms : 2559 net assigned charge : 6.800004 assigned positive charge : 410.3224 centred at (gu) : 90.46313 88.14109 81.93819 assigned negative charge : -403.5234 centred at (gu) : 90.32457 87.65576 82.54872 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 152945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24308 grid for indexing accessible points = 1.400000 m= 75579 mr = 109726 m= 24503 mr = 60734 m= 4699 mr = 18899 m= 542 mr = 3299 m= 10 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1376 time to turn everything in is 0.8100000 number of dielectric boundary points 65312 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 20463 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) : 1.734076 object centre at (A) : 23.64450 17.05100 16.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.032691 7.8634612E-02 midg,1,midg; midg,igrid,midg -8.1551738E-02 1.5877606E-02 1,midg,midg; igrid,midg,midg -0.2877569 7.6128311E-02 gauss-seidel spectral radius is 0.9991878 estimated iterations to convergence 277 setup time was (sec) 1.030000 now iterating at: 14:04:09 rms-change max change #iterations 9.089317 258.2199 at 10iterations 5.252048 126.6513 at 20iterations 3.015316 71.16101 at 30iterations 1.724744 36.21384 at 40iterations 0.9794492 22.21622 at 50iterations 0.5561984 12.45715 at 60iterations 0.3140353 6.355804 at 70iterations 0.1770291 3.439629 at 80iterations 0.1000222 1.989920 at 90iterations 5.6172572E-02 1.164581 at 100iterations 3.1679414E-02 0.6570969 at 110iterations 1.7839333E-02 0.3517799 at 120iterations 1.0071705E-02 0.2021208 at 130iterations 5.7064183E-03 0.1232529 at 140iterations 3.2692482E-03 6.7104340E-02 at 150iterations 1.9073018E-03 4.6401978E-02 at 160iterations 1.1500547E-03 3.1929016E-02 at 170iterations 7.3081854E-04 1.9756317E-02 at 180iterations finished qdiffx linear iterations at : 14:04:20 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 7.3081854E-04 1.9756317E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 14:04:20 12.165u 0.204s 0:12.68 97.4% 0+0k 0+0io 0pf+0w