Sat Oct 15 11:26:35 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 11:26:35 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 0.6038504 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): -61.40300 -2.448000 ymin,ymax (A): -24.91000 27.20800 zmin,zma (A): -10.10500 43.48100 x,y,z range (A): 58.95500 52.11800 53.58600 scale (grids/A): 0.6038504 object centre (A): -31.92550 1.149000 16.68800 number of atom coordinates read : 3016 total number of charged atoms : 2872 net assigned charge : 1.000014 assigned positive charge : 451.1392 centred at (gu) : 91.67923 89.97505 90.07130 assigned negative charge : -450.1403 centred at (gu) : 91.73714 89.95870 90.06345 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7288 nv = 96 ne = 84 npr = 62089 no. pairs analyzed = 62089 no. exposed pairs = 3474 no. arc points = 24162 no. surface atoms = 1180 nbur = 1836 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= 324 mr = 4148 m= 0 mr = 36 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2300000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2477 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 9080 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6102285E-10 9.2302421E-10 midg,1,midg; midg,igrid,midg -2.4354088E-10 1.3039898E-09 1,midg,midg; igrid,midg,midg 2.2374707E-09 -3.3145633E-09 gauss-seidel spectral radius is 0.9858348 estimated iterations to convergence 69 setup time was (sec) 0.5100000 now iterating at: 11:26:36 rms-change max change #iterations 0.1239681 18.23851 at 10iterations 1.1039292E-02 1.521677 at 20iterations 1.0726695E-03 0.1508522 at 30iterations 1.3545672E-04 1.8981934E-02 at 40iterations 2.2984999E-05 2.9602051E-03 at 50iterations finished qdiffx linear iterations at : 11:26:39 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 2.2984999E-05 2.9602051E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 11:26:40 4.117u 0.300s 0:04.98 88.5% 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 Sat Oct 15 2011 at 11:26:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 1.811551 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): -61.40300 -2.448000 ymin,ymax (A): -24.91000 27.20800 zmin,zma (A): -10.10500 43.48100 x,y,z range (A): 58.95500 52.11800 53.58600 scale (grids/A): 1.811551 object centre (A): -31.92550 1.149000 16.68800 number of atom coordinates read : 3016 total number of charged atoms : 2872 net assigned charge : 1.000014 assigned positive charge : 451.1392 centred at (gu) : 95.03654 89.92442 90.21339 assigned negative charge : -450.1403 centred at (gu) : 95.21118 89.87592 90.19013 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24162 grid for indexing accessible points = 1.400000 m= 27901 mr = 57609 m= 3546 mr = 20485 m= 141 mr = 2122 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2624 time to turn everything in is 0.4200000 number of dielectric boundary points 31712 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22453 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) : 0.6038504 object centre at (A) : -31.92550 1.149000 16.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7922410E-03 -1.9521089E-02 midg,1,midg; midg,igrid,midg 2.1939415E-03 1.2176513E-02 1,midg,midg; igrid,midg,midg 2.7737493E-02 2.3891362E-03 gauss-seidel spectral radius is 0.9985309 estimated iterations to convergence 207 setup time was (sec) 0.7200000 now iterating at: 11:26:41 rms-change max change #iterations 4.172957 153.3531 at 10iterations 1.895925 60.41053 at 20iterations 0.8659034 28.10007 at 30iterations 0.3929321 11.79945 at 40iterations 0.1796729 5.667167 at 50iterations 8.2293466E-02 2.859756 at 60iterations 3.7392344E-02 1.105692 at 70iterations 1.7138459E-02 0.5016651 at 80iterations 7.8373505E-03 0.2475433 at 90iterations 3.6047383E-03 0.1306639 at 100iterations 1.6627671E-03 5.1010132E-02 at 110iterations 7.7472540E-04 2.5985718E-02 at 120iterations finished qdiffx linear iterations at : 11:26:52 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 7.7472540E-04 2.5985718E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 11:26:52 9.793u 0.379s 0:12.17 83.4% 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 11:26:52 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 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: 2.717327 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): -61.40300 -2.448000 ymin,ymax (A): -24.91000 27.20800 zmin,zma (A): -10.10500 43.48100 x,y,z range (A): 58.95500 52.11800 53.58600 scale (grids/A): 2.717327 object centre (A): -31.92550 1.149000 16.68800 number of atom coordinates read : 3016 total number of charged atoms : 2872 net assigned charge : 1.000014 assigned positive charge : 451.1392 centred at (gu) : 97.55451 89.88648 90.32004 assigned negative charge : -450.1403 centred at (gu) : 97.81667 89.81377 90.28506 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 186659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24162 grid for indexing accessible points = 1.400000 m= 93134 mr = 139873 m= 30471 mr = 76568 m= 6201 mr = 24241 m= 668 mr = 4624 m= 27 mr = 417 m= 0 mr = 11 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 9021 time to turn everything in is 1.130000 number of dielectric boundary points 71426 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 22973 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) : 1.811551 object centre at (A) : -31.92550 1.149000 16.68800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0666830E-02 -0.2399161 midg,1,midg; midg,igrid,midg -9.4548082E-03 0.1470173 1,midg,midg; igrid,midg,midg 0.3275081 0.1370313 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.440000 now iterating at: 11:26:54 rms-change max change #iterations 9.969993 386.0950 at 10iterations 5.782302 119.8956 at 20iterations 3.332764 74.30804 at 30iterations 1.911915 38.12032 at 40iterations 1.099198 22.00193 at 50iterations 0.6279774 12.87199 at 60iterations 0.3599280 6.944731 at 70iterations 0.2055468 4.008915 at 80iterations 0.1173727 2.115798 at 90iterations 6.7080870E-02 1.513302 at 100iterations 3.8337011E-02 0.6966047 at 110iterations 2.1856353E-02 0.3999786 at 120iterations 1.2493151E-02 0.2226410 at 130iterations 7.1414849E-03 0.1297345 at 140iterations 4.0956787E-03 7.8375340E-02 at 150iterations 2.3612259E-03 4.5982361E-02 at 160iterations 1.3699598E-03 2.5295258E-02 at 170iterations 8.0261764E-04 1.4785767E-02 at 180iterations finished qdiffx linear iterations at : 11:27:10 total time elapsed so far: 15.35000 # loops : 180 mean,max change (kT/e) : 8.0261764E-04 1.4785767E-02 energy calculations done at 15.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.49000 DelPhi exited at 11:27:10 15.487u 0.348s 0:17.84 88.6% 0+0k 0+0io 0pf+0w