Sat Oct 15 11:21:12 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 Sat Oct 15 2011 at 11:21:12 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 450 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6094743 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): 13.34500 71.75600 ymin,ymax (A): 7.193000 63.92000 zmin,zma (A): 20.83200 64.31300 x,y,z range (A): 58.41100 56.72700 43.48100 scale (grids/A): 0.6094743 object centre (A): 42.55050 35.55650 42.57250 number of atom coordinates read : 2681 total number of charged atoms : 2538 net assigned charge : -2.957992 assigned positive charge : 416.2978 centred at (gu) : 91.31798 92.51599 90.97612 assigned negative charge : -419.2563 centred at (gu) : 91.33349 92.39950 90.98798 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6383 nv = 96 ne = 84 npr = 54536 no. pairs analyzed = 54536 no. exposed pairs = 3348 no. arc points = 24680 no. surface atoms = 1124 nbur = 1557 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3241 m= 0 mr = 27 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3100000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2479 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8073 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0028159E-09 -3.0616216E-09 midg,1,midg; midg,igrid,midg -4.5740371E-09 7.5040987E-09 1,midg,midg; igrid,midg,midg -7.9274132E-10 -3.5625796E-09 gauss-seidel spectral radius is 0.9860717 estimated iterations to convergence 69 setup time was (sec) 0.5500000 now iterating at: 11:21:13 rms-change max change #iterations 0.1239788 23.17480 at 10iterations 1.0793929E-02 1.846863 at 20iterations 9.3780580E-04 0.1546879 at 30iterations 8.4841224E-05 1.3393402E-02 at 40iterations 7.5338075E-06 1.2621880E-03 at 50iterations finished qdiffx linear iterations at : 11:21:15 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 7.5338075E-06 1.2621880E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 11:21:16 3.349u 0.168s 0:03.81 91.8% 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 Sat Oct 15 2011 at 11:21:16 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 450 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.828423 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): 13.34500 71.75600 ymin,ymax (A): 7.193000 63.92000 zmin,zma (A): 20.83200 64.31300 x,y,z range (A): 58.41100 56.72700 43.48100 scale (grids/A): 1.828423 object centre (A): 42.55050 35.55650 42.57250 number of atom coordinates read : 2681 total number of charged atoms : 2538 net assigned charge : -2.957992 assigned positive charge : 416.2978 centred at (gu) : 93.95354 97.54759 92.92757 assigned negative charge : -419.2563 centred at (gu) : 94.00025 97.19819 92.96342 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70040 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24680 grid for indexing accessible points = 1.400000 m= 22570 mr = 46370 m= 3073 mr = 15912 m= 148 mr = 1790 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 712 time to turn everything in is 0.5100000 number of dielectric boundary points 31731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19773 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) : 0.6094743 object centre at (A) : 42.55050 35.55650 42.57250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2725626E-03 -1.6698962E-02 midg,1,midg; midg,igrid,midg -7.4558053E-03 1.8565102E-02 1,midg,midg; igrid,midg,midg 7.4009388E-03 -2.6881391E-02 gauss-seidel spectral radius is 0.9985264 estimated iterations to convergence 207 setup time was (sec) 0.8100000 now iterating at: 11:21:17 rms-change max change #iterations 4.112815 152.8383 at 10iterations 1.854791 66.52821 at 20iterations 0.8418972 30.17884 at 30iterations 0.3820030 13.26355 at 40iterations 0.1731811 6.224762 at 50iterations 7.8661330E-02 2.523544 at 60iterations 3.5671663E-02 1.155368 at 70iterations 1.6249038E-02 0.5458205 at 80iterations 7.3670936E-03 0.2634239 at 90iterations 3.3464571E-03 0.1083641 at 100iterations 1.5281898E-03 5.7907104E-02 at 110iterations 6.9256540E-04 2.5791168E-02 at 120iterations finished qdiffx linear iterations at : 11:21:23 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 6.9256540E-04 2.5791168E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 11:21:24 7.446u 0.228s 0:08.05 95.1% 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 Sat Oct 15 2011 at 11:21:24 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 !!! WARNING: HIR 440 has a net charge of 0.5140 !!! WARNING: HIR 444 has a net charge of 0.5140 !!! WARNING: HIR 450 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.742634 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): 13.34500 71.75600 ymin,ymax (A): 7.193000 63.92000 zmin,zma (A): 20.83200 64.31300 x,y,z range (A): 58.41100 56.72700 43.48100 scale (grids/A): 2.742634 object centre (A): 42.55050 35.55650 42.57250 number of atom coordinates read : 2681 total number of charged atoms : 2538 net assigned charge : -2.957992 assigned positive charge : 416.2978 centred at (gu) : 95.92995 101.3212 94.39132 assigned negative charge : -419.2563 centred at (gu) : 96.00035 100.7973 94.44513 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 162275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24680 grid for indexing accessible points = 1.400000 m= 75086 mr = 113197 m= 24722 mr = 59825 m= 5223 mr = 19146 m= 666 mr = 3749 m= 23 mr = 432 m= 0 mr = 5 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 2457 time to turn everything in is 1.230000 number of dielectric boundary points 71641 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 20300 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) : 1.828423 object centre at (A) : 42.55050 35.55650 42.57250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3336638E-02 -0.2537606 midg,1,midg; midg,igrid,midg -6.9348313E-02 0.3757046 1,midg,midg; igrid,midg,midg 0.1165791 -0.3136537 gauss-seidel spectral radius is 0.9992309 estimated iterations to convergence 285 setup time was (sec) 1.540000 now iterating at: 11:21:26 rms-change max change #iterations 9.837929 436.9276 at 10iterations 5.679599 133.4378 at 20iterations 3.267496 69.91750 at 30iterations 1.862020 35.05719 at 40iterations 1.064478 22.81937 at 50iterations 0.6050125 11.99311 at 60iterations 0.3438404 6.279618 at 70iterations 0.1951375 3.941528 at 80iterations 0.1108784 2.100497 at 90iterations 6.2749259E-02 1.212020 at 100iterations 3.5659354E-02 0.6987057 at 110iterations 2.0270489E-02 0.3692169 at 120iterations 1.1495067E-02 0.2190466 at 130iterations 6.5237801E-03 0.1267929 at 140iterations 3.6923878E-03 7.0050716E-02 at 150iterations 2.0976923E-03 3.9378643E-02 at 160iterations 1.1952025E-03 2.3426056E-02 at 170iterations 6.7553477E-04 1.3364792E-02 at 180iterations finished qdiffx linear iterations at : 11:21:36 total time elapsed so far: 11.96000 # loops : 180 mean,max change (kT/e) : 6.7553477E-04 1.3364792E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.14000 DelPhi exited at 11:21:37 12.141u 0.210s 0:12.82 96.3% 0+0k 0+0io 0pf+0w